bluuebunny/crossref_metadata_2025 huggingface dataset:
Good moms: dependent-young and their mothers cope better than others with longer dry season in plains zebras
Authors: Thel Lucie , Bonenfant Christophe , Chamaillé-Jammes Simon
Published: October 2021

In large herbivores, the timing of births often coincides with the seasonal peak of food resources availability, likely to improve juvenile survival and reduce reproduction costs. Some species however, breed year-round, even in seasonal environments. Demographic processes, such as to what extent being born during the lean season reduces survival of juveniles and reproductive females, remain understudied in large mammals inhabiting tropical ecosystems. We investigated survival rates in plains zebras (Equus quagga) in Hwange National Park (Zimbabwe), a highly seasonal savanna ecosystem. We used capture-recapture models to analyse long-term demographic data (2008-2019). We investigated the effect of seasonality as a categorical (wet versus dry season) and continuous (duration of the dry season) variable on survival. We found little variability in early juvenile survival (φ = 0.458 ± 0.044 SE, < 6 m.o.), whereas late juvenile and yearling survival was higher and decreased with increasing length of the dry season (from 0.850 ± 0.095 SE to 0.480 ± 0.120 SE). Female survival was high (> 0.703 ± 0.057 SE and up to 0.995 ± 0.006 SE) but decreased with increasing exposure to the dry season in non-reproductive females. The probability of females becoming reproductive in the following year was not affected by the length of the dry season (0.423 and 0.420 for reproductive and non-reproductive females respectively). Our results highlight the importance of individual quality in reproductive performance, as reproductive females seem to buffer the effect of environmental variability on their own survival and that of their foal.
Cross-border investigations on the prevalence and transmission dynamics of Cryptosporidium species in dairy cattle farms in western mainland Europe
Authors: Pinto Pedro , Ribeiro Cláudia A. , Hoque Sumaiya , Hammouma Ourida , Leruste Hélène , Detriche Sébastien , Canniere Evi , Daandels Yvonne , Dellevoet Martine , Roemen Janine , Bourgeois Anne Barbier , Kváč Martin , Follet Jérôme , Tsaousis Anastasios D.
Published: October 2021

Cryptosporidium is comprised an apicomplexan parasitic protist, which infects a wide range of hosts, causing cryptosporidiosis. In cattle farms, the incidence of cryptosporidiosis results in high mortality in calves leading to considerable economic loss in the livestock industry. Infected animals may also act as a major reservoir of Cryptosporidium spp., in particular C. parvum, the most common cause of cryptosporidiosis in calves. This poses a significant risk to other farms via breeding centres, to trading of livestock and to human health. This study, funded by the Interreg-2-seas programme, is a part of a global project aimed at strategies to tackle cryptosporidiosis. To reach this target, it was essential to determine whether prevalence was dependent on the studied countries or if the issue was borderless. Indeed, C. parvum occurrence was assessed across dairy farms in certain regions of Belgium, France and the Netherlands. At the same time, the animal-to-animal transmission of the circulating C. parvum subtypes was studied. To accomplish this, 1084 faecal samples, corresponding to 57 dairy-farms from all three countries, were analysed. Well-established protocols amplifying the 18S rDNA and gp60 genes fragments, followed by DNA sequencing, were used for the detection and subtyping C. parvum; the DNA sequences obtained were further characterised using a combination of bioinformatics and phylogenetics methods. Our results show 25.7%, 24.9% and 20.8% prevalence of Cryptosporidium spp. in Belgium, France and the Netherlands respectively. Overall, 93% of the farms were Cryptosporidium positive. The gp60 subtyping demonstrated a significant number of the C. parvum positives belonged to the IIa allelic family, which has been also detected in humans. Consequently, this study highlights how widespread is C. parvum in dairy farms and endorses cattle as a major carrier of zoonotic C. parvum subtypes, which subsequently pose a significant threat to human health.
Adjusting for Common Variant Polygenic Scores Improves Yield in Rare Variant Association Analyses
Authors: Jurgens Sean J. , Pirruccello James P. , Choi Seung Hoan , Morrill Valerie N. , Chaffin Mark , Lubitz Steven A. , Lunetta Kathryn L. , Ellinor Patrick T.
Published: October 2021

With the emergence of large-scale sequencing data, methods for improving power in rare variant analyses (RVAT) are needed. Here, we show that adjusting for common variant polygenic scores improves the yield in gene-based RVAT across 65 quantitative traits in the UK Biobank (up to 20% increase at α=2.6×10−6), without a marked increase in false-positive rates or genomic inflation. Our results illustrate how adjusting for common variant effects can aid in rare variant association discovery.
Chronic alcohol drinking persistently suppresses thalamostriatal excitation of cholinergic neurons to impair cognitive flexibility
Authors: Ma Tengfei , Huang Zhenbo , Xie Xueyi , Cheng Yifeng , Zhuang Xiaowen , Childs Matthew , Gangal Himanshu , Wang Xuehua , Smith Laura , Smith Rachel , Zhou Yubin , Wang Jun
Published: October 2021

Exposure to addictive substances impairs flexible decision-making. Cognitive flexibility is mediated by striatal cholinergic interneurons (CINs). However, how chronic alcohol drinking alters cognitive flexibility through CINs remains unclear. Here, we report that chronic alcohol consumption and withdrawal impaired reversal of instrumental learning. Chronic alcohol consumption and withdrawal also caused a long-lasting (21 d) reduction of excitatory thalamic inputs onto CINs and reduced pause response of CINs in the dorsomedial striatum (DMS). CINs are known to inhibit glutamatergic transmission in dopamine D1 receptor-expressing medium spiny neurons (D1-MSNs) but facilitate this transmission in D2-MSNs, which may contribute to flexible behavior. We discovered that chronic alcohol drinking impaired CIN-mediated inhibition in D1-MSNs and facilitation in D2-MSNs. Importantly, in vivo optogenetic induction of long-term potentiation of thalamostriatal transmission in DMS CINs rescued alcohol-induced reversal learning deficits. These results demonstrate that chronic alcohol drinking reduces thalamic excitation of DMS CINs, compromising their regulation of glutamatergic transmission in MSNs, which may contribute to alcohol-induced impairment of cognitive flexibility. These findings provide a neural mechanism underlying inflexible drinking in alcohol use disorder.
Mitochondrial Haplogroup Association with Fasting Glucose Response in African Americans Treated with a Thiazide Diuretic
Authors: Minniefield Bre A. , Armstrong Nicole D. , Srinivasasainagendra Vinodh , Tiwari Hemant K. , Ballinger Scott W. , Chong Zechen , Aslibekyan Stella , Arnett Donna K. , Irvin Marguerite R.
Published: October 2021

Hypertensive African Americans have ~50% response rate to thiazide diuretic treatment. This contributes to a high prevalence of uncontrolled high blood pressure. Here, we examine the role the mitochondrial genome has on thiazide diuretic treatment response in hypertensive African Americans enrolled in a clinical trial. Participants from the Antihypertensive and Lipid Lowering Treatment to Prevent Heart Attack Trial (ALLHAT, n= 4279) were genotyped using the Illumina Infinium Multi-Ethnic Beadchip. Haplotype groups were called using HaploGrep. We used linear regression analysis to examine the association between mitochondrial haplogroups (L, M, and N) and change in blood pressure and change in fasting glucose over 6 months and two years, respectively. The analysis revealed a null association between mitochondrial haplogroups M and N vs. L for each of the outcomes. In subgroup analysis, the L subclades L1, L2, and L3/L4 (vs. L0) were each inversely associated with fasting glucose response (p < 0.05). This discovery analysis suggests the mitochondrial genome has a small effect on fasting glucose but not blood pressure response to thiazide diuretic treatment in African Americans.
Rapid and Effective Inactivation of SARS-CoV-2 by a Cationic Conjugated Oligomer with Visible Light: Studies of Antiviral Activity in Solutions and on Supports
Authors: Kaya Kemal , Khalil Mohammed I. , Fetrow Benjamin , Fritz Hugh , Jagadesan Pradeepkumar , Bondu Virginie , Ista Linnea , Chi Eva Y. , Schanze Kirk S. , Whitten David G. , Kell Alison M.
Published: October 2021

This paper presents results of a study of a new cationic oligomer that contains end groups and a chromophore affording inactivation of SARS-Cov-2 by visible light irradiation in solution or as a solid coating on wipes paper and glass fiber filtration substrates. A key finding of this study is that the cationic oligomer with a central thiophene ring and imidazolium charged groups give outstanding performance in both killing of E. coli bacterial cells and inactivation of the virus at very short times. Our introduction of cationic N-Methyl Imidazolium groups enhances the light-activation process for both E. coli and SARS-Cov-2 but dampens the dark killing of the bacteria and eliminates the dark inactivation of the virus. For the studies with this oligomer in solution at concentration of 1 μg/mL and E. coli we obtain 3 log killing of the bacteria with 10 min irradiation with LuzChem cool white lights (mimicking indoor illumination). With the oligomer in solution at a concentration of 10 μg/mL, we observe 4 logs inactivation (99.99 %) in 5 minutes of irradiation and total inactivation after 10 min. The oligomer is quite active against E. coli on oligomer-coated wipes papers and glass fiber filter supports. The SARS-Cov-2 is also inactivated by the oligomer coated glass fiber filter papers. This study indicates that these oligomer-coated materials may be very useful as wipes and filtration materials.
Precision localization of cellular proteins with fluorescent Fab-based probes
Authors: Liccardo F. , Lo Monte M. , Corrado B. , Veneruso M. , Celentano S. , Coscia M.R. , Coppola G. , Pucci P. , Palumbo G. , Luini A. , Lampe M. , Marzullo V.M.
Published: October 2021

Currently, a major technical limitation of microscopy based image analysis is the linkage error – which describes the distance between e.g. the target epitope of cellular protein to the fluorescence emitter, which position is finally detected in a microscope. With continuously improving resolution of today’s (super-resolution) microscopes, the linkage errors can severely hamper the correct interpretation of images and is usually introduced in experiments by the use of standard intracellular staining reagents such as fluorescently labelled antibodies. The linkage error of standard labelled antibodies is caused by the size of the antibody and the random distribution of fluorescent emitters on the antibody surface. Together, these two factors account for a fluorescence displacement of ~40nm when staining proteins by indirect immunofluorescence; and ~20nm when staining with fluorescently coupled primary antibodies. In this study, we describe a class of staining reagents that effectively reduce the linkage error by more than five-fold when compared to conventional staining techniques. These reagents, called Fluo-N-Fabs, consist of an antigen binding fragment of a full-length antibody (Fab / fragment antigen binding) that is selectively conjugated at the N-terminal amino group with fluorescent organic molecules, thereby reducing the distance between the fluorescent emitter and the protein target of the analysis. Fluo-N-Fabs also exhibit the capability to penetrate tissues and highly crowded cell compartments, thus allowing for the efficient detection of cellular epitopes of interest in a wide range of fixed samples. We believe this class of reagents realize an unmet need in cell biological super resolution imaging studies where the precise localization of the target of interest is crucial for the understanding of complex biological phenomena.
Comparative linkage mapping uncovers massive chromosomal inversions that suppress recombination between locally adapted fish populations
Authors: Akopyan Maria , Tigano Anna , Jacobs Arne , Wilder Aryn P. , Baumann Hannes , Therkildsen Nina O.
Published: October 2021

The role of recombination in genome evolution has long been studied in theory, but until recently empirical investigations had been limited to a small number of model species. Here we compare the recombination landscape and genome collinearity between two populations of the Atlantic silverside (Menidia menidia), a small fish distributed across the steep latitudinal climate gradient of the North American Atlantic coast. Using ddRADseq, we constructed separate linkage maps for locally adapted populations from New York and Georgia and their inter-population lab cross. First, we used one of the linkage maps to improve the current silverside genome assembly by anchoring three large unplaced scaffolds to two chromosomes. Second, we estimated sex-specific recombination rates, finding 2.75-fold higher recombination rates in females than males—one of the most extreme examples of heterochiasmy in a fish. While recombination occurs relatively evenly across female chromosomes, it is restricted to only the terminal ends of male chromosomes. Furthermore, comparisons of female linkage maps revealed suppressed recombination along several massive chromosomal inversions spanning nearly 16% of the genome and segregating between locally adapted populations. Finally, we discerned significantly higher recombination rates across chromosomes in the northern population. In addition to providing valuable resources for ongoing evolutionary and comparative genomic studies, our findings represent a striking example of structural variation that impacts recombination between adaptively divergent populations, providing empirical support for theorized genomic mechanisms facilitating adaptation despite gene flow.
Identification of a specific biomarker ofAcinetobacter baumanniiGlobal Clone 1 by machine learning and PCR related to metabolic fitness of ESKAPE pathogens
Authors: Álvarez Verónica Elizabeth , Quiroga María Paula , Centrón Daniela
Published: October 2021

Since the emergence of high-risk clones worldwide, constant investigations have been undertaken to comprehend the molecular basis that led to their prevalent dissemination in nosocomial settings over time. So far, the complex and multifactorial genetic traits of this type of epidemic clones have only allowed the identification of biomarkers with low specificity. A machine learning algorithm was able to recognize unequivocally a biomarker for the early and accurate detection ofAcinetobacter baumanniiGlobal Clone 1 (GC1), one of the most disseminated high-risk clones. Support Vector Machine identified the U1 sequence with 367 nucleotides length that matched a fragment of themoaCBgene, which encodes the molybdenum cofactor biosynthesis C and B proteins. U1 differentiates specifically betweenA. baumanniiGC1 and non-GC1 strains, becoming a suitable biomarker capable of being translated into clinical settings as a molecular typing method for early diagnosis based on PCR as shown here. Since the metabolic pathways of Mo enzymes have been recognized as putative therapeutic targets for ESKAPE pathogens, our findings highlighted that machine learning can be also useful in intricate knowledge gaps of high-risk clones and implies noteworthy support to the literature to identify challenging nosocomial biomarkers for other multidrug-resistant high-risk clones.

IMPORTANCE

A. baumanniiGC1 is an important high-risk clone that rapidly develops extreme drug resistance in the nosocomial niche. Furthermore, several strains were identified worldwide in environmental samples exacerbating the risk of human interactions. Early diagnosis is mandatory to limit its dissemination and to outline appropriate antibiotic stewardship schedules. A region of 367 bp length (U1) within themoaCBgene not subjected to Lateral Genetic Transfer or to antibiotic pressures was successfully found by Support Vector Machine algorithm that predictsA. baumanniiGC1 strains. PCR assays have confirmed that U1 specifically identifiesA. baumanniiGC1 strains. At the same time, research on the group of Mo enzymes proposed this metabolic pathway related to superbuǵs metabolism as a potential future drug target site for ESKAPE pathogens due to its central role in bacterial fitness during infection. These findings confirmed the importance of machine learning applied to the burden of the rise of antibiotic resistance.
Triazolopyrimidines target aerobic respiration in Mycobacterium tuberculosis
Authors: Shelton Catherine , McNeil Matthew , Flint Lindsay , Russell Dara , Berube Bryan , Korkegian Aaron , Ovechkina Yulia , Parish Tanya
Published: October 2021

We previously identified a series of triazolopyrimidines with anti-tubercular activity. We determined that Mycobacterium tuberculosis strains with mutations in a component of the cytochrome bc1 system (QcrB) were resistant to the series. A cytochrome bd oxidase deletion strain was also more sensitive to this series. We isolated resistant mutants, all of which had mutations in Rv1339. Compounds were active against intracellular bacteria but did not inhibit mitochondrial respiration in human HepG2 cells. These data are consistent with triazolopyrimidines acting via inhibition of M. tuberculosis QcrB.
Genome-wide association study of 1,391 plasma metabolites in 6,136 Finnish men identifies 303 novel signals and provides biological insights into human diseases
Authors: Yin Xianyong , Chan Lap Sum , Bose Debraj , Jackson Anne U. , VandeHaar Peter , Locke Adam E. , Fuchsberger Christian , Stringham Heather M. , Yu Ketian , Silva Lilian Fernandes , Service Susan K. , Zhang Daiwei , Hector Emily C. , Young Erica , Ganel Liron , Das Indraniel , Abel Haley , Erdos Michael R. , Bonnycastle Lori L. , Kuusisto Johanna , Stitziel Nathan O. , Hall Ira , Wagner Gregory R. ,   FinnGen, Kang Jian , Morrison Jean , Burant Charles F. , Collins Francis S. , Ripatti Samuli , Palotie Aarno , Freimer Nelson B. , Mohlke Karen L. , Scott Laura J. , Wen Xiaoquan , Fauman Eric B. , Laakso Markku , Boehnke Michael
Published: October 2021

Few studies have explored the impact of rare variants (minor allele frequency, MAF<1%) on highly heritable plasma metabolites identified in metabolomic screens. The Finnish population provides an ideal opportunity for such explorations, given the multiple bottlenecks and expansions that have shaped its history, and the enrichment for many otherwise rare alleles that has resulted. Here, we report genetic associations for 1,391 plasma metabolites in 6,136 men from the late-settlement region of Finland. We identify 303 novel association signals, more than one third at variants rare or enriched in Finns. Many of these signals identify genes not previously implicated in metabolite genome-wide association studies and suggest mechanisms for diseases and disease-related traits.
Ambient heat exposure and COPD hospitalisations in England: A nationwide case-crossover study during 2007-2018
Authors: Konstantinoudis Garyfallos , Minelli Cosetta , Vicedo Cabrera Ana Maria , Ballester Joan , Gasparrini Antonio , Blangiardo Marta
Published: October 2021

Background

There is emerging evidence suggesting a link between ambient heat exposure and chronic obstructive pulmonary disease (COPD) hospitalisations. Individual and contextual characteristics can affect population vulnerabilities to COPD hospitalisation due to heat exposure. This study quantifies the effect of ambient heat on COPD hospitalisations and examines population vulnerabilities by age, sex, and contextual characteristics.

Methods

Individual data on COPD hospitalisation at high geographical resolution (postcodes) during 2007-2018 in England was retrieved from the small area health statistics unit. Maximum temperature at 1 km×1km resolution was available from the UK Met Office. We employed a case-cross over study design and fitted Bayesian conditional Poisson regression models. We adjusted for relative humidity and national holidays, and examined effect modification by age, sex, green space, average temperature, deprivation and urbanicity.

Results

After accounting for confounding, we found a 1.47% (95% Credible Interval 1.19% to 1.73%), increase in the hospitalisation risk for every 1°C increase in temperatures above 23.2°C (lags 0-2 days). We reported weak evidence of an effect modification by sex and age. We found a strong spatial determinant of the COPD hospitalisation risk due to heat exposure, that was alleviated when we accounted for contextual characteristics. 1 851 (95% CrI 1 576 to 2 079) COPD hospitalisations were associated with temperatures above 23.2°C annually.

Conclusion

Our study suggests that resources should be allocated to support the public health systems, for instance through developing or expanding heat-health alerts, to challenge the increasing future heat-related COPD hospitalisation burden.

Key Messages

What is the key question?

What is the short-term effect of heat exposure on COPD hospitalisation and which contextual/societal factors affect population vulnerability?

What is the bottom line?

For every 1°C increase in summer temperatures higher than 23.2°C, the risk of COPD hospitalisation increases by 1.47%, and populations in the North and in the South East are more vulnerable.

Why read on?

This large nationwide study in England using individual data quantifies the effect of heat exposure on COPD hospitalisations; these findings inform future policies regarding preparedness and resilience of public health systems against the increasing COPD burden due to the increasing temperatures.
SARS-CoV-2 Transmission and Impacts of Unvaccinated-Only Screening in Populations of Mixed Vaccination Status
Authors: Bubar Kate M. , Middleton Casey E. , Bjorkman Kristen K. , Parker Roy , Larremore Daniel B.
Published: October 2021

Community testing programs focused on the unvaccinated population are being enacted in populations with mixed vaccination status to mitigate SARS-CoV-2 spread. Presumably, these policies assume that the unvaccinated are driving transmission, though it is not well understood how viral spread occurs in mixed-status populations. Here, we analyze a model of transmission in which a variable fraction of the population is vaccinated, with unvaccinated individuals proactively screened for infection. By exploring a range of transmission rates, vaccine effectiveness (VE) scenarios, and rates of prior infection, this analysis reveals principles of viral spread in communities of mixed vaccination status, with implications for screening policies. As vaccination rates increase, the proportion of transmission driven by the unvaccinated population decreases, such that most community spread is driven by breakthrough infections once vaccine coverage exceeds 55% (omicron) or 80% (delta), with additional variation dependent on waning or boosted VE. More broadly, the potential impacts of unvaccinated-only screening fall into three distinct parameter regions: (I) “flattening the curve” with little impact on cumulative infections, (II) effectively suppressing transmission, and (III) negligible impact because herd immunity is reached without screening. By evaluating a wide range of scenarios, this work finds broadly that effective mitigation of SARS-CoV-2 transmission by unvaccinated-only screening is highly dependent on vaccination rate, population-level immunity, screening compliance, and vaccine effectiveness against the current variant.
Neutralization of Mu and C.1.2 SARS-CoV-2 Variants by Vaccine-elicited Antibodies in Individuals With and Without Previous History of Infection
Authors: Tada Takuya , Zhou Hao , Dcosta Belinda M. , Samanovic Marie I. , Cornelius Amber , Herati Ramin S. , Mulligan Mark J. , Landau Nathaniel R.
Published: October 2021

Recently identified SARS-CoV-2 variants Mu and C.1.2 have mutations in the receptor binding domain and N- and C-terminal domains that might confer resistance to natural and vaccine-elicited antibody. Analysis with pseudotyped lentiviruses showed that viruses with the Mu and C.1.2 spike proteins were partially resistant to neutralization by antibodies in convalescent sera and those elicited by mRNA and adenoviral vector-based vaccine-elicited antibodies. Virus with the C.1.2 variant spike, which is heavily mutated, was more neutralization-resistant than that of any of variants of concern. The resistance of the C.1.2 spike was caused by a combination of the RBD mutations N501Y, Y449H and E484K and the NTD mutations. Although Mu and C.1.2 were partially resistant to neutralizing antibody, neutralizing titers elicited by mRNA vaccination remained above what is found in convalescent sera and thus are likely to remain protective against severe disease. The neutralizing titers of sera from infection-experienced BNT162b2-vaccinated individuals, those with a history of previous SARS-CoV-2 infection, were as much as 15-fold higher than those of vaccinated individuals without previous infection and effectively neutralized all of the variants. The findings demonstrate that individuals can raise a broadly neutralizing humoral response by generating a polyclonal response to multiple spike protein epitopes that should protect against current and future variants.
Optimal Precision and Accuracy in 4Pi-STORM using Dynamic Spline PSF Models
Authors: Bates Mark , Keller-Findeisen Jan , Przybylski Adrian , Hüper Andreas , Stephan Till , Ilgen Peter , Cereceda Delgado Angel R. , D’Este Elisa , Jakobs Stefan , Sahl Steffen J. , Hell Stefan W.
Published: October 2021

Dual-objective 4Pi fluorescence detection enables single molecule localization microscopy, e.g. PALM and STORM, with sub-10 nanometer spatial resolution in 3D. Despite its outstanding sensitivity, wider application of this technique has been hindered by complex instrumentation requirements and the challenging nature of the data analysis. The point spread function (PSF) of the 4Pi optical system is difficult to model, leading to periodic image artifacts and compromised resolution. In this work we report the development of a 4Pi-STORM microscope which obtains improved resolution and accuracy by modeling the 4Pi PSF dynamically, while using a simpler optical design. We introduce dynamic spline PSF models, which incorporate fluctuations in the modulation phase of the experimentally determined PSF, capturing the temporal dynamics of the optical system. Our method reaches the theoretical limits for localization precision while largely eliminating phase-wrapping artifacts, by making full use of the information content of the data. With a 3D precision as high as 2 – 3 nanometers, 4Pi-STORM achieves new levels of image detail, and extends the range of biological questions that can be addressed by fluorescence nanoscopy, as we demonstrate by investigating protein and nucleic acid organization in primary neurons and mammalian mitochondria.
Base editors for citrus gene editing
Authors: Huang Xiaoen , Wang Yuanchun , Wang Nian
Published: October 2021

Base editors, such as adenine base editors (ABE) and cytosine base editors (CBE), provide alternatives for precise genome editing without generating double-strand breaks (DSBs), thus avoiding the risk of genome instability and unpredictable outcomes caused by DNA repair. Precise gene editing mediated by base editors in citrus has not been reported. Here, we have successfully adapted the ABE to edit the TATA box in the promoter region of the canker susceptibility gene LOB1 from TATA to CACA in grapefruit (Citrus paradise) and sweet orange (Citrus sinensis). TATA-edited plants are resistant to the canker pathogen Xanthomonas citri subsp. citri (Xcc). In addition, CBE was successfully used to edit the acetolactate synthase (ALS) gene in citrus. ALS-edited plants were resistant to the herbicide chlorsulfuron. Two ALS-edited plants did not show green fluorescence although the starting construct for transformation contains a GFP expression cassette. The Cas9 gene was undetectable in the herbicide-resistant citrus plants. This indicates that the ALS edited plants are transgene-free, representing the first transgene-free gene-edited citrus using the CRISPR technology. In summary, we have successfully adapted the base editors for precise citrus gene editing. The CBE base editor has been used to generate transgene-free citrus via transient expression.
Expanding the pool of public controls for GWAS via a method for combining genotypes from arrays and sequencing
Authors: Mathur Ravi , Fang Fang , Gaddis Nathan , Hancock Dana B. , Cho Michael H. , Hokanson John E. , Bierut Laura J. , Lutz Sharon M. , Young Kendra , Smith Albert V. ,   NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Silverman Edwin K. , Page Grier P. , Johnson Eric O.
Published: October 2021

Genome-wide association studies (GWAS) have made impactful discoveries for complex diseases, often by amassing very large sample sizes. Yet, GWAS of many diseases remain underpowered, especially for non-European ancestries. One cost-effective approach to increase sample size is to combine existing case-only cohorts with public controls, but this approach is limited by the need for a large overlap in variants across genotyping arrays and the scarcity of non-European controls. We developed and validated a protocol, Genotyping Array-WGS Merge (GAWMerge), for combining genotypes from arrays and whole genome sequencing, ensuring complete variant overlap, and allowing for diverse samples like Trans-Omics for Precision Medicine to be used. Our protocol involves phasing, imputation, and filtering. We illustrated its ability to control type I error and recover known disease-associated signals across technologies, independent datasets, and ancestries in smoking-related cohorts. GAWMerge enables genetic studies to leverage existing cohorts to validly increase sample size and enhance discovery.
Similar geographic patterns but distinct assembly processes of abundant and rare bacterioplankton communities in river networks of the Taihu Basin
Authors: Xu Sai
Published: October 2021

Bacterioplankton play an important role in the biochemical cycling in rivers. The dynamics of hydrologic conditions in rivers were believed to affect geographic pattern and assembly process of these microorganisms, which have not been widely investigated. In this study, the geographic pattern and community assembly process of bacterioplankton in river networks of the Taihu Basin were systematically explored using amplicon sequencing of the 16S rRNA gene. The results showed that community structure, diversity, and taxonomic composition of bacterioplankton all exhibited significant temporal variation during wet, normal, and dry seasons (p<0.01). The neutral community model and null model were applied to reveal the assembly process of bacterioplankton community. The stochastic process and deterministic process both shaped the bacterioplankton community with greater influence of deterministic process. In addition, the abundant and rare bacterioplankton communities were comparatively analyzed. The abundant and rare bacterioplankton communities exhibited similar temporal dynamics (principal coordinates analysis) and spatial variations (distance-decay relationship), indicating similar geographic patterns. Meanwhile, distinct assembly processes were observed for the abundant and rare bacterioplankton communities. Stochastic process (dispersal limitation) shaped the abundant bacterioplankton community while deterministic process (heterogeneous selection) dominated the assembly process of rare bacterioplankton community. Mantel test, redundancy analysis, and correlation analysis together indicated that pH and dissolved oxygen were the major environmental attributes that affected the bacterioplankton community structure and assembly process. These results expanded our understanding of the geographic patterns, assembly processes, and driving factors of the bacterioplankton community in river networks and provided clues provided clues for the underlying mechanisms.
Integrative system biology analysis of barley transcriptome – hormonal signaling against biotic stress
Authors: Soltani Zahra , Moghadam Ali , Tahmasebi Ahmad , Niazi Ali
Published: October 2021

Biotic stresses are environmental factors that cause a variety of crop diseases and damages. In contrast, crops trigger specific transduction signaling pathways that the hormones are the central players. Integrative OMICS for systems genetic engineering approach contributes in the understanding of molecular mechanisms. In this research, the system biology approaches were applied to discover particular molecular interactions between biotic stresses and hormonal signaling in barley. The meta-analysis of the data identified a total of 1232 and 304 differentially expressed genes (DEGs) respectively so that were significantly involved in defense processes and hormone signaling. A total of 24 TFs belonged to 15 conserved families and 6 TFs belonged to 6 conserved families were identified for biotic and hormonal data respectively, whereas NF-YC, GNAT, and whirly families were the most abundant groups. The functional analysis of the upstream regions for over-represented cis-acting elements revealed that were involved activation of transcription factors in response to pathogens and hormones. Based on the co-expression analysis, 6 and 7 distinct co-expression modules related to biotic stresses and hormonal signaling were respectively uncovered. The gene network analysis also identified novel hub genes such as TIM10, DRT101, ADG1, and TRA2 which may be involved in regulating defense responses to biotic stresses. In addition, many new genes with unknown function were obtained. Since this study represents a first preliminary curated system biology analysis of barley transcriptomic responses to biotic stresses and hormone treatments, introduces important candidate genes that may be beneficial to crop biotechnologists to accelerate genetic engineering programs.
Multiple Sex Chromosome Drivers in a Mammal with Three Sex Chromosomes
Authors: Saunders Paul A. , Perez Julie , Ronce Ophélie , Veyrunes Frédéric
Published: October 2021

A few mammals have unusual sex determining systems whereby fertile XY females live alongside XX females and XY males. These systems are regarded as evolutionary paradoxes because of the production of sex-reversed individuals and non-viable embryos, but they nevertheless seem stable over evolutionary time. Several hypotheses have been proposed to account for their stability, including models involving sex chromosome drive (i.e., biased transmission of sex chromosomes to the next generation). Here we corroborate this hypothesis inMus minutoides, a close relative of the house mouse in which the presence of XY females is due to the evolution of a third sex chromosome: a feminizing X. Through extensive molecular sexing of pups at weaning, we reveal the existence of a remarkable male sex chromosome drive system in this species, whereby direction and strength of drive is conditional upon the genotype of males’ partners: males transmit their Y to almost 80% of their offspring when mating with XX females, and only 36% when mating with XY females. Using mathematical modelling, we explore the joint evolution of these unusual sex-determining and drive systems, revealing that different sequences of events could have led to the evolution of this bizarre system, and that the “conditional” nature of sex chromosome drive stabilizes the feminizing X, and even precludes a return to a standard XX/XY system.
Knock-down of a regulatory barcode shifts macrophage polarization destination from M1 to M2 and increases pathogen burden uponS. aureusinfection
Authors: Ravichandran Sathyabaarathi , Bhatt Bharat , Shah Awantika , Balaji Kithiganahalli Narayanaswamy , Chandra Nagasuma
Published: October 2021

Macrophages are driven to form distinct functional phenotypes in response to different immunological stimuli, in a process widely referred to as macrophage polarization. Transcriptional regulators that guide macrophage polarization in response to a given trigger remain largely unknown. In this study, we interrogate the programmable landscape in macrophages to find regulatory panels that determine the precise polarization state that a macrophage is driven to. Towards this, we configure an integrative network analysis pipeline that utilizes macrophage transcriptomes in response to 28 distinct stimuli and reconstructs contextualized human gene regulatory networks, and identifies epicentres of perturbations in each case. We find that these contextualized regulatory networks form a spectrum of thirteen distinct clusters with M1 and M2 at the two ends. Using our computational pipeline, we identify combinatorial panels of epicentric regulatory factors (RFs) for each polarization state. We demonstrate that a set of three RFs i.e.,CEBPB,NFE2L2andBCL3, is sufficient to change the polarization destination from M1 to M2. siRNA knockdown of the 3-RF set in THP1 derived M0 cells, despite exposure to an M1 stimulant, significantly attenuated the shift to M1 phenotype, and instead increased the expression of M2 markers. Single knockdown of each RF also showed a similar trend. The siRNA-mediated knockdown of the 3-RF set rendered the macrophages hyper-susceptible toStaphylococcus aureusinfection, demonstrating the importance of these factors in modulating immune responses. Overall, our results provide insights into the transcriptional mechanisms underlying macrophage polarization and identify key regulatory factors that may be targeted to modulate immune responses.
Overexpression of Zinc finger (GpZF) promotes drought tolerance in grass pea (Lathyrus sativus)
Authors: Parsa Mitra , Kashanchi Mona , Zeinali Amineh , pourfakhraei Elaheh
Published: October 2021

The genes encoding Cys2/His2-type zinc finger proteins constitute a large family in higher plants consisting of a family of plant transcription factors. GpZF encodes a Cys2/His2-type zinc finger protein. The purposes of this study are to elucidate further the functions of a novel zinc finger transcription factor in the grass pea (GpZF) gene involved in the drought stress response in the grass pea (Lathyrus sativus) and to investigate its biochemical and physiological parameters under stress conditions. GpZF was expressed in grass pea. Relative gene expression analysis showed the GpZF gene in independent transgenic lines was more under drought mild and severe treatments (50% and 25% field capacity-FC). Furthermore, overexpression of this gene in grass pea results in more relative water content, free proline, and soluble sugars than the wild-type (WT) plants under 50% and 25% FC stresses. Moreover, in 25% FC, the independent transgenic lines revealed an increase in survival rates and dry weight than the WT plants. GpZF thus implies the positive role in drought stress tolerance in Lathyrus sativus. In conclusion, the transgenic grass pea plants generated in this study could be used to farm arid areas.

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GpZF is a positive regulator in drought stress tolerance in grass pea.
Multi-hallmark long noncoding RNA maps reveal non-small cell lung cancer vulnerabilities
Authors: Esposito Roberta , Polidori Taisia , Meise Dominik F. , Pulido-Quetglas Carlos , Chouvardas Panagiotis , Forster Stefan , Schaerer Paulina , Kobel Andrea , Schlatter Juliette , Roemmele Michaela , Westemeier Emily S. , Zhu Lina , Lanzós Andrés , Guillen-Ramirez Hugo A. , Basile Giulia , Carrozzo Irene , Vancura Adrienne , Ullrich Sebastian , Andrades Alvaro , Harvey Dylan , Medina Pedro P. , Ma Patrick C. , Haefliger Simon , Wang Xin , Martinez Ivan , Ochsenbein Adrian , Riether Carsten , Johnson Rory
Published: October 2021

Long noncoding RNAs (lncRNAs) are widely dysregulated in cancer, yet their functional roles in cellular disease hallmarks remain unclear. Here we employ pooled CRISPR deletion to perturb all 831 lncRNAs in KRAS-mutant non-small cell lung cancer (NSCLC), and measure their contribution to proliferation, chemoresistance and migration across two cell backgrounds. Integrative analysis of this data outperforms conventional “dropout” screens in identifying cancer genes, while prioritising disease-relevant lncRNAs with pleiotropic and background-independent roles. Altogether 60 high-confidence oncogenic lncRNAs are active in NSCLC, the majority identified here for the first time, and which tend to be amplified and overexpressed in tumours. A follow-up antisense oligonucleotide (ASO) screen shortlisted two candidates, Cancer Hallmarks in Lung LncRNA (CHiLL 1&2), whose knockdown consistently suppressed cancer hallmarks in a variety of 2D and 3D tumour models. Molecular phenotyping reveals that CHiLL 1&2 control cellular-level phenotypes via distinct transcriptional networks converging on common oncogenic pathways. In summary, this work reveals a multi-dimensional functional lncRNA landscape underlying NSCLC that contains potential therapeutic vulnerabilities.
Design, 3D-printing, and characterisation of a low-cost, open-source centrifuge adaptor for separating large volume clinical blood samples
Authors: Haque Md Ehtashamul , Marriott Linda , Naeem Noman , Henry Taygan , Conde Alvaro J. , Kersaudy-Kerhoas Maïwenn
Published: October 2021

Blood plasma separation is a prerequisite in numerous biomedical assays involving low abundance plasma-borne biomarkers and thus is the fundamental step before many bioanalytical steps. Conventionally, plasma separation is performed using high-capacity refrigerated centrifuges which have the advantage of handling large volume blood samples. These centrifuges are bulky, and prohibitively expensive for low-resource settings, with prices starting from $1,500. Although commercial and existing open-source micro-centrifuges are relatively low-cost, they cannot handle large volume blood samples. Microfluidic blood plasma separation also has been adopted by many researchers to enable low-cost plasma separation, however, these systems still present yield and purity issues for extremely low abundance biomarker detection such as the detection of various fractions of circulating cell-free DNA. To overcome this, we customised the rotor of a commercially available micro-centrifuge ∼$125) using fused filament fabrication to enable centrifugation of large clinical blood samples in resource poor-settings. Our designed adaptor ($15) can hold two 9 mL S-Monovette tubes and maintain the same separation performance (yield, cell count, hemolysis, albumin levels) as the control benchtop refrigerated centrifuge. This low-cost open-source centrifugation system capable of processing clinical blood tubes could be valuable to low-funded laboratories or low-resource settings where centrifugation is required immediately after blood withdrawal for further testing.
Chromosome-encoded IpaH ubiquitin ligases indicate non-human pathogenic Escherichia
Authors: Dranenko Natalia O. , Tutukina Maria , Gelfand Mikhail S. , Kondrashov Fyodor A. , Bochkareva Olga O.
Published: October 2021

Until recently, Shigella and enteroinvasive Escherichia coli were thought to be primate-restricted pathogens. The base of their pathogenicity is the type 3 secretion system (T3SS) encoded by the pINV virulence plasmid, which facilitates host cell invasion and subsequent proliferation. A large family of T3SS effectors, E3 ubiquitin-ligases encoded by the ipaH genes, have a key role in the Shigella pathogenicity through the modulation of cellular ubiquitination that degrades host proteins. However, recent genomic studies identified ipaH genes in the genomes of Escherichia marmotae, a potential marmot pathogen, and an E. coli extracted from fecal samples of bovine calves, suggesting that non-human hosts may also be infected by these strains, potentially pathogenic to humans.

We performed a comparative genomic study of the functional repertoires in the ipaH gene family in Shigella and enteroinvasive Escherichia from human and predicted non-human hosts. We found that fewer than half of Shigella genomes had a complete set of ipaH genes, with frequent gene losses and duplications that were not consistent with the species tree and nomenclature. Non-human host IpaH proteins had a diverse set of substrate-binding domains and, in contrast to the Shigella proteins, two different types of the NEL C-terminal domain. Only the ipaH9.8 gene was found in Escherichia derived from both human and non-human hosts. These results provide a framework for understanding of ipaH-mediated host-pathogens interactions and suggest a need for a genomic study of fecal samples from diseased animals.
A specific role for Importin-5 and NASP in the import and nuclear hand-off of monomeric H3
Authors: Pardal Alonso J. , Bowman Andrew J.
Published: October 2021

Core histones package chromosomal DNA and regulate genomic transactions, with their nuclear import and deposition involving importin-β proteins and a dedicated repertoire of histone chaperones. Previously, a histone H3-H4 dimer has been isolated bound to Importin-4 (Imp4) and and the chaperone ASF1, suggesting H3 and H4 fold together in the cytoplasm before nuclear import. However, other studies have shown the existence of monomeric H3 in the nucleus, indicating a post import folding pathway. Here we report that the predominant importin associated with cytoplasmic H3 is Importin-5 (Imp5), which hands-off its monomeric cargo to nuclear sNASP. Imp5, in contrast to Imp4, binds to both H3 and H4 containing constitutively monomeric mutations and binds to newly synthesised, monomeric H3 tethered in the cytoplasm. Constitutively monomeric H3 retains its interaction with NASP, whereas monomeric H4 retains interactions specifically with HAT1 and RBBP7. High-resolution separation of NASP interactors shows the ‘s’ isoform but not the ‘t’ isoform associates with monomeric H3, whilst both isoforms associate with H3-H4 dimers in at least three discrete multi-chaperoning complexes. In vitro binding experiments show mutual exclusivity between sNASP and Imp5 in binding H3, suggesting direct competition for interaction sites, with the GTP-bound form of Ran required for histone transfer. Finally, using pulse-chase analysis we show that cytoplasm-tethered histones do not interact with endogenous NASP until they reach the nucleus, whereupon they bind rapidly. We propose an Imp5-specific import pathway for monomeric H3 that hands off to sNASP in the nucleus, with a parallel H4 pathway involving Imp5 and the HAT1-RBBP7 complex, followed by nuclear folding and hand-off to deposition factors.