bluuebunny/crossref_metadata_2025 huggingface dataset:
Expansion of nickel binding- and histidine-rich proteins during gastric adaptation of Helicobacter species
Authors: Fischer Frédéric , Vorontsov Egor , Turlin Evelyne , Malosse Christian , Garcia Camille , Tabb David L , Chamot-Rooke Julia , Percudani Riccardo , Vinella Daniel , De Reuse Hilde
Published: August 2022

Acquisition and homeostasis of essential metals during host colonization by bacterial pathogens rely on metal uptake, trafficking, and storage proteins. How these factors have evolved within bacterial pathogens is poorly defined. Urease, a nickel enzyme, is essential for Helicobacter pylori to colonize the acidic stomach. Our previous data suggest that acquisition of nickel transporters and a histidine-rich protein (HRP) involved in nickel storage in H. pylori and gastric Helicobacter spp. have been essential evolutionary events for gastric colonization. Using bioinformatics, proteomics, and phylogenetics, we extended this analysis to determine how evolution has framed the repertoire of HRPs among 39 Epsilonproteobacteria; 18 gastric and 11 non-gastric enterohepatic (EH) Helicobacter spp., as well as 10 other Epsilonproteobacteria. We identified a total of 213 HRPs distributed in 22 protein families named orthologous groups (OGs) with His-rich domains, including 15 newly described OGs. Gastric Helicobacter spp. are enriched in HRPs (7.7 ± 1.9 HRPs/strain) as compared to EH Helicobacter spp. (1.9 ± 1.0 HRPs/strain) with a particular prevalence of HRPs with C-terminal histidine-rich domains in gastric species. The expression and nickel-binding capacity of several HRPs was validated in five gastric Helicobacter spp. We established the evolutionary history of new HRP families, such as the periplasmic HP0721-like proteins and the HugZ-type heme oxygenases. The expansion of histidine-rich extensions in gastric Helicobacter spp. proteins is intriguing but can tentatively be associated with the presence of the urease nickel enzyme. We conclude that this HRP expansion is associated with unique properties of organisms that rely on large intracellular nickel amounts for their survival.
Safety and patterns of survivorship in recurrent GBM following resection and surgically targeted radiation therapy: Results from a prospective trial
Authors: Smith Kris , Nakaji Peter , Thomas Theresa , Pinnaduwage Dilini , Wallstrom Garrick , Choi Mehee , Zabramski Joseph , Chen Clark , Brachman David
Published: August 2022

Background

Treatment of recurrent glioblastoma (GBM) remains problematic with survival after additional therapy typically less than 12 months. We prospectively evaluated whether outcomes might be improved with resection plus permanent implantation of a novel radiation device utilizing the gamma-emitting isotope Cs-131 embedded within bioresorbable collagen tiles.

Methods

Recurrent histologic GBM were treated in a single-arm trial. Following radiation, the surgical bed was lined with the tiles. Subsequent treatments were at the treating physician’s discretion.

Results

28 patients were treated (20 at first recurrence, range 1–3). Median age was 58 years, KPS was 80, female:male ratio was 10:18. Methylguanine methyltransferase (MGMT) was methylated in 11%, unmethylated in 18%, and unknown in 71%. Post implant, 17 patients (61%) received ≥1 course of systemic therapy. For all patients, Kaplan-Meier estimates of median time to local failure were 12.1 months, post-implant survival was 10.7 months for all patients and 15.1 months for patients who received systemic therapy; for all patients, median overall survival from diagnosis was 25.0 months (range 9.1–143.1). Sex, age, and number of prior progressions were not statistically significant. Local control was continuously maintained in 46% of patients. Two deaths within 30 days occurred, one from intracranial hemorrhage and one after persistent coma. Three symptomatic adverse events occurred: one wound infection requiring surgery and two late radiation brain injury, resolved non-surgically.

Conclusion

This pre-commercial trial demonstrated acceptable safety and favorable post-treatment local control and survival. The device has received FDA clearance for use in newly diagnosed malignant and all recurrent intracranial neoplasms.
Cat Scratch Disease: 9 Years of Experience at a Pediatric Center
Authors: Amin Omayma , Rostad Christina A , Gonzalez Mark , Rostad Bradley S , Caltharp Shelley , Quincer Elizabeth , Betke Briana A , Gottdenker Nicole L , Wilson Jonathan J , Shane Andi L , Elmontser Mohnd , Camacho-Gonzalez Andres , Senior Tal , Smith Oliver , Anderson Evan J , Yildirim Inci
Published: August 2022

Background

A more complete understanding of the epidemiology, risk factors, and clinical features of cat scratch disease (CSD) in children could help guide patient care.

Methods

We conducted a retrospective analysis of children presenting to a tertiary pediatric hospital system in Atlanta, Georgia between January 1, 2010 and December 31, 2018 who had serology, polymerase chain reaction, and/or cytopathological results consistent with a Bartonella henselae infection. We also retrospectively reviewed veterinary diagnostic results performed at the University of Georgia from 2018 to 2020 to ascertain the burden of bartonellosis in companion animals within the state.

Results

We identified 304 children with CSD over 9 years with the largest proportion of diagnoses made during August (41 of 304, 13.5%) and September (47 of 304, 15.5%). The median age of child cases was 8.1 years (interquartile range [IQR], 5.4–12.1); 156 (51.3%) were female; 242 of 262 (92.4%) reported feline exposure; and 55 of 250 (22%) reported canine exposure of those with exposure histories documented in the medical record. Although lymphadenopathy was present on physical examination in the majority of cases (78.8%), atypical presentations lacking lymphadenopathy were also common (63 of 304, 20.7%). Among children with radiographic imaging, 20 of 55 (36.4%) had splenomegaly and 21 of 55 (38.1%) had splenic and/or hepatic microabscesses. Among veterinary data, Bartonella seroprevalence was 12 of 146 (8.2%), all among canines, with a geographic distribution that spanned the state of Georgia.

Conclusions

Distinguishing clinical features of CSD included subacute regional lymphadenopathy in school-aged children in the late summer, almost all of whom had cat exposure. Atypical clinical manifestations of CSD were also commonly identified.
Understanding forced internal displacement in Ukraine: insights and lessons for today’s crises
Authors: Mykhnenko Vlad , Delahaye Elliot , Mehdi Nigel
Published: August 2022

The contribution of this paper is threefold: first, it accounts for the problem of Ukraine’s forced internal displacement, following the Russian occupation of the Crimea and Donbas regions in 2014; second, this study applies a number of quantitative research methods to provide new insights into the way that individual and destination characteristics of the internally displaced people (IDPs) impact upon their destination preferences; finally, it draws four key policy lessons for dealing with today’s worst humanitarian catastrophe in Europe since 1945. These lessons focus on the individual characteristics of forced migrants for understanding displacement patterns; and the need for full restoration of legitimate democratic government at home as the necessary condition for return. They also highlight that in the extraordinary circumstances of large-scale warfare, life-saving action takes precedence over any other motivations; and the host communities’ perceived sympathy towards the forced migrants’ home nation ultimately determines the choice of settlement.
ECERIFERUM1-6A is required for the synthesis of cuticular wax alkanes and promotes drought tolerance in wheat
Authors: He Jiajia , Li Chongzhao , Hu Ning , Zhu Yuyao , He Zhaofeng , Sun Yulin , Wang Zhonghua , Wang Yong
Published: August 2022

Cuticular waxes cover the aerial surfaces of land plants and protect them from various environmental stresses. Alkanes are major wax components and contribute to plant drought tolerance, but the biosynthesis and regulation of alkanes remain largely unknown in wheat (Triticum aestivum L.). Here, we identified and functionally characterized a key alkane biosynthesis gene ECERIFERUM1-6A (TaCER1-6A) from wheat. The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated knockout mutation in TaCER1-6A greatly reduced the contents of C27, C29, C31, and C33 alkanes in wheat leaves, while TaCER1-6A overexpression significantly increased the contents of these alkanes in wheat leaves, suggesting that TaCER1-6A is specifically involved in the biosynthesis of C27, C29, C31, and C33 alkanes on wheat leaf surfaces. TaCER1-6A knockout lines exhibited increased cuticle permeability and reduced drought tolerance, whereas TaCER1-6A overexpression lines displayed reduced cuticle permeability and enhanced drought tolerance. TaCER1-6A was highly expressed in flag leaf blades and seedling leaf blades and could respond to abiotic stresses and abscisic acid. TaCER1-6A was located in the endoplasmic reticulum, which is the subcellular compartment responsible for wax biosynthesis. A total of three haplotypes (HapI/II/III) of TaCER1-6A were identified in 43 wheat accessions, and HapI was the dominant haplotype (95%) in these wheat varieties. Additionally, we identified two R2R3-MYB transcription factors TaMYB96-2D and TaMYB96-5D that bound directly to the conserved motif CAACCA in promoters of the cuticular wax biosynthesis genes TaCER1-6A, TaCER1-1A, and fatty acyl-CoA reductase4. Collectively, these results suggest that TaCER1-6A is required for C27, C29, C31, and C33 alkanes biosynthesis and improves drought tolerance in wheat.
Gender, police-community contacts, and situational outcomes
Authors: Nowacki Jeffrey S , Makin David , Willits Dale , Parks Megan , Brooks Rachael
Published: August 2022

Recent research in policing focuses on the nature of the police-citizen interaction itself. However, little of this research prioritizes the role that community member gender plays in these interactions. We examine how gender can influence a range of police outcomes including de-escalation and procedurally just policing behaviors. Using body-worn camera (BWC) footage from over 700 police-community member encounters, this study examines how gender, along with other situational factors including contact type, guardianship, and levels of resistance influence a range of police outcomes. Findings indicate that while gender did not directly influence police action, other situational characteristics of police encounters did. Police training protocols should focus on how police can account for some of these characteristics to improve decision-making and increase use of de-escalation techniques.
Comparison of mucormycosis infection between patients with and without a history of COVID-19 infection: a retrospective cohort study
Authors: Saadi Mohammad Hassan Gholampoor , Hosseini Seyed Ali , Khodamoradi Zohre , Mokhtaryan Maryam , Omidifar Navid , Moghadami Mohsen
Published: August 2022

Background

Mucormycosis infection is a complication seen in some coronavirus disease 2019 (COVID-19) patients. This study compares the characteristics of mucormycosis infection between COVID-19 and non-COVID-19 patients.

Methods

This retrospective cohort comprised 87 patients with mucormycosis divided into two groups. The first included 44 patients who had COVID-19 recently before hospitalization due to mucormycosis at Namazi Hospital, Shiraz, Iran, between February 2019 and August 2021. The second group included all 43 patients hospitalized at the same hospital due to mucormycosis between 2010 and 2019 (pre-pandemic).

Results

Mucormycosis patients with a history of recent COVID-19 infection had a higher rate of diabetes mellitus, fewer malignancies and higher blood glucose, erythrocyte sedimentation rate and C-reactive protein levels (p<0.05). Glucocorticoid use was common (77%) in the COVID-19 group.

Conclusions

In the pre-COVID-19 era, mucormycosis mainly affected immunodeficient patients like those receiving chemotherapy due to malignancy but now seems to affect COVID-19 patients with uncontrolled blood glucose and glucocorticoids use. Special care must be taken in prescribing glucocorticoids and controlling the blood glucose levels of COVID-19 patients.
Genomic surveillance of Salmonella spp. in the Philippines during 2013–2014
Authors: Lagrada Marietta L , Argimón Silvia , Borlasa Janice B , Abad Jaywardeen P , Gayeta June M , Masim Melissa L , Olorosa Agnettah M , Cohen Victoria , Jeffrey Benjamin , Abudahab Khalil , Sia Sonia B , Hufano Charmian M , Stelling John , Holden Matthew T G , Aanensen David M , Carlos Celia C
Published: August 2022

Background

Increasing antimicrobial resistance (AMR) in Salmonella has been observed in the Philippines. We aimed to characterise the population and AMR mechanisms of Salmonella with whole genome sequencing (WGS) and compare it with laboratory surveillance methods.

Methods

The serotype, multilocus sequence type, AMR genes and relatedness between isolates were determined from the genomes of 148 Salmonella Typhi (S. Typhi) and 65 non-typhoidal Salmonella (NTS) collected by the Antimicrobial Resistance Surveillance Program during 2013–2014. Genotypic serotypes and AMR prediction were compared with phenotypic data.

Results

AMR rates in S. Typhi were low, with sparse acquisition of mutations associated with reduced susceptibility to fluoroquinolones or extended-spectrum beta-lactamases (ESBL) genes. By contrast, 75% of NTS isolates were insusceptible to at least one antimicrobial, with more than half carrying mutations and/or genes linked to fluoroquinolone resistance. ESBL genes were detected in five genomes, which also carried other AMR determinants. The population of S. Typhi was dominated by likely endemic genotype 3.0, which caused a putative local outbreak. The main NTS clades were global epidemic S. Enteritidis ST11 and S. Typhimurium monophasic variant (I,4,[5],12: i: -) ST34.

Conclusion

We provide the first genomic characterisation of Salmonella from the Philippines and evidence of WGS utility for ongoing surveillance.
Lineage BA.2 dominated the Omicron SARS-CoV-2 epidemic wave in the Philippines
Authors: Li Yao-Tsun , Polotan Francisco Gerardo M , Sotelo Gerald Ivan S , Alpino Anne Pauline A , Dolor Ardiane Ysabelle M , Tujan Ma. Angelica A , Gomez Ma. Ricci R , Onza Othoniel Jan T , Chang Angela Kae T , Bautista Criselda T , Carandang June C , Yangzon Maria Sofia L , Pangilinan Elcid Aaron R , Mantaring Renato Jacinto , Telles Alyssa Joyce E , Egana John Michael C , Endozo Joshua Jose S , Cruz Rianna Patricia S , Tablizo Francis A , Yap Jan Michael C , Maralit Benedict A , Ayes Marc Edsel C , de la Paz Eva Marie C , Saloma Cynthia P , Lim Dodge R , Dancel Lei Lanna M , Uy-Lumandas Mayan , Medado Inez Andrea P , Dizon Timothy John R , Hampson Katie , Daldry Simon , Hughes Joseph , Brunker Kirstyn
Published: August 2022

The Omicron severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant led to a dramatic global epidemic wave following detection in South Africa in November 2021. The BA.1 Omicron lineage was dominant and responsible for most SARS-CoV-2 outbreaks in countries around the world during December 2021–January 2022, while other Omicron lineages, including BA.2, accounted for the minority of global isolates. Here, we describe the Omicron wave in the Philippines by analysing genomic data. Our results identify the presence of both BA.1 and BA.2 lineages in the Philippines in December 2021, before cases surged in January 2022. We infer that only the BA.2 lineage underwent sustained transmission in the country, with an estimated emergence around 18 November 2021 (95 per cent highest posterior density: 6–28 November), while despite multiple introductions, BA.1 transmission remained limited. These results suggest that the Philippines was one of the earliest areas affected by BA.2 and reiterate the importance of whole genome sequencing for monitoring outbreaks.
Effects of Fungicides and Cultivar Resistance on Fusarium Head Blight and Deoxynivalenol in Spring Barley from 2014 to 2019
Authors: Friskop Andrew , Halvorson Jessica , Hansen Bryan , Meyer Scott , Jordahl Jim , Gautam Pravin , Chapara Venkata , Arens Amanda , Tjelde Tyler , Kalil Audrey , Fonseka Dmitri , Schatz Blaine , Brueggeman Robert , Baldwin Thomas , Gross Pat , Deplazes Chad , Ransom Joel
Published: August 2022

Spring barley production and quality in the United States is severely impacted by Fusarium head blight (FHB), primarily caused by Fusarium graminearum. Management of FHB is best accomplished using an integrated approach including resistant varieties and fungicides. Field experiments were established from 2014 to 2019 to quantify the effects of host resistance, fungicide, and fungicide timing on management of FHB and deoxynivalenol (DON) and yield protection in spring barley. Three separate research objectives were investigated using multiyear and multilocation experiments. These included investigating the efficacy of prothioconazole + tebuconazole applied at either Feekes growth stage (FGS) 10.5 (full head) or 3 to 7 days after FGS 10.5; the efficacy of sequential fungicide applications occurring at both FGS 10.5 and 3 to 7 days after FGS 10.5 using prothioconazole + tebuconazole, metconazole, prothioconazole, or tebuconazole; and the efficacy and timing of pydiflumetofen + propiconazole. Pooled analysis results suggest that metconazole, prothioconazole + tebuconazole, and pydiflumetofen + propiconazole are all effective fungicides for reducing DON, reducing FHB, and protecting yield. The use of sequential fungicide applications with one occurring at FGS 10.5 and another at 3 to 7 days after FGS 10.5 provided greater suppression than a single application at FGS 10.5. The greatest DON reduction from pydiflumetofen + propiconazole occurred when applied at full head or 3 to 7 days after full head. Across all research objectives, the most effective single fungicide application timing to reduce FHB, reduce DON, and protect yield in barley is 3 to 7 days after FGS 10.5.
Activation of α6-containing GABAA receptors induces antinociception under physiological and pathological conditions
Authors: Rodríguez-Palma Erick J. , De la Luz-Cuellar Yarim E. , Islas-Espinoza Ana M. , Félix-Leyva Adalberto E. , Shiers Stephanie I. , García Guadalupe , Torres-López Jorge E. , Delgado-Lezama Rodolfo , Murbartián Janet , Price Theodore J. , Granados-Soto Vinicio
Published: August 2022

The loss of GABAergic inhibition is a mechanism that underlies neuropathic pain. Therefore, rescuing the GABAergic inhibitory tone through the activation of GABAA receptors is a strategy to reduce neuropathic pain. This study was designed to elucidate the function of the spinal α6-containing GABAA receptor in physiological conditions and neuropathic pain in female and male rats. Results show that α6-containing GABAA receptor blockade or transient α6-containing GABAA receptor knockdown induces evoked hypersensitivity and spontaneous pain in naive female rats. The α6 subunit is expressed in IB4+ and CGRP+ primary afferent neurons in the rat spinal dorsal horn and dorsal root ganglia but not astrocytes. Nerve injury reduces α6 subunit protein expression in the central terminals of the primary afferent neurons and dorsal root ganglia, whereas intrathecal administration of positive allosteric modulators of the α6-containing GABAA receptor reduces tactile allodynia and spontaneous nociceptive behaviors in female, but not male, neuropathic rats and mice. Overexpression of the spinal α6 subunit reduces tactile allodynia and restores α6 subunit expression in neuropathic rats. Positive allosteric modulators of the α6-containing GABAA receptor induces a greater antiallodynic effect in female rats and mice compared with male rats and mice. Finally, α6 subunit is expressed in humans. This receptor is found in CGRP+ and P2X3+ primary afferent fibers but not astrocytes in the human spinal dorsal horn. Our results suggest that the spinal α6-containing GABAA receptor has a sex-specific antinociceptive role in neuropathic pain, suggesting that this receptor may represent an interesting target to develop a novel treatment for neuropathic pain.
Diffusion Tensor Imaging as a Tool to Evaluate the Cognitive Function of Patients With Vascular Dementia
Authors: Zhang Qiuchi , Yan Xiwu , Du Jun , Chen Zhaoyao , Chang Cheng
Published: August 2022

Background:

Vascular dementia (VaD) is the most common type of dementia secondary to Alzheimer’s disease. The pathologic mechanism of VaD is complex, and VaD still lacks a more objective diagnosis and evaluation method. Diffusion tensor imaging (DTI) can better detect the organizational structure and functional characteristics compared with any other diagnosis methods. Therefore, DTI has broad application in evaluating the severity and prognosis of VaD. This study aimed to assess the value of DTI in evaluating the cognitive function of patients with VaD.

Methods:

Authors searched Pubmed, Embase, and Cochrane Library, using the search terms, such as “diffusion tensor imaging”, “DTI”, “Vascular Dementia”, “Arteriosclerotic Dementia”, “Cognition”, and “Cognitive”. A voxel-based meta-analysis combined with quality statistics was performed, using the anisotropic effect-size version of the signed differential mapping method.

Results:

A total of 8 case-control studies were included in this meta-analysis. The sample size of patients ranged from 35 to 60, including 166 patients in the VaD group and 177 healthy individuals. The DTI imaging of the brain tissue of VaD patients was significantly different from that of healthy individuals.

Conclusions:

DTI imaging of the brain tissue of VaD patients was clearly different from that of healthy controls. Therefore it may be feasible to use DTI imaging as a diagnostic method for VaD.
Prevalence and Clinico-Radiologic Spectrum of Intracranial Atherosclerotic Disease-Related Stroke
Authors: Zafar Azra , Albakr Aishah , Shahid Rizwana , Alkhamis Fahd , Alabdali Majed , Aljaafari Danah , Nazish Saima , Ishaque Noman , Soltan Nehad Mahmoud , Msmar Amir H. , Al-Suhibani Sari Saleh , Al-Jehani Hosam
Published: August 2022

Background:

Intracranial atherosclerotic disease (ICAD) is an important etiologic subtype of acute ischemic stroke (AIS). However, little direct evidence is available regarding ICAD-related stroke in Saudi Arabia (SA). This study aimed to identify the prevalence and describe the clinico-radiological spectrum of ICAD-related AIS in a SA cohort.

Methods:

This was a hospital-based retrospective study enrolling patients with ICAD-related AIS between 2017 and 2020. The electronic charts were reviewed. The mechanisms of stroke were identified as artery-to-artery embolization (AAE), in situ thrombotic occlusion, hypoperfusion, or perforator branch occlusion. Pearson’s χ2 test was performed to calculate the P values to establish the statistical significance of factors that could correlate with the mechanisms of stroke and functional outcome.

Results:

ICAD was found in 133 of AIS comprising 26% of total. Data from all patients were reviewed. Left ICA (25%) was the most frequently affected vessel. Territorial pattern (63.9%) was the most common infarct pattern, and AAE (44.3%) was the most common underlying mechanism. Perforator branch occlusion was more prevalent in women than in men. Malignant and hemorrhagic transformation (P=0.00) were more prevalent in the AAE group. Left-sided vascular involvement was statistically associated with unfavorable outcomes than the right (P=0.019).

Conclusions:

The prevalence of ICAD in our cohort from Western Asia did not differ from that in Southern Asia. ICA involvement was observed more frequently than previously reported. Further research from SA is required to better understand ICAD-related strokes in this region.
Dynamic switching of lateral inhibition spatial patterns
Authors: Hawley Joshua , Manning Cerys , Biga Veronica , Glendinning Paul , Papalopulu Nancy
Published: August 2022

Hes genes are transcriptional repressors activated by Notch. In the developing mouse neural tissue, HES5 expression oscillates in neural progenitors (Manning
et al.
2019
Nat. Commun.
10
, 1–19 (
doi:10.1038/s41467-019-10734-8
)) and is spatially organized in small clusters of cells with synchronized expression (microclusters). Furthermore, these microclusters are arranged with a spatial periodicity of three–four cells in the dorso-ventral axis and show regular switching between HES5 high/low expression on a longer time scale and larger amplitude than individual temporal oscillators (Biga
et al.
2021
Mol. Syst. Biol.
17
, e9902 (
doi:10.15252/msb.20209902
)). However, our initial computational modelling of coupled HES5 could not explain these features of the experimental data. In this study, we provide theoretical results that address these issues with biologically pertinent additions. Here, we report that extending Notch signalling to non-neighbouring progenitor cells is sufficient to generate spatial periodicity of the correct size. In addition, introducing a regular perturbation of Notch signalling by the emerging differentiating cells induces a temporal switching in the spatial pattern, which is longer than an individual cell’s periodicity. Thus, with these two new mechanisms, a computational model delivers outputs that closely resemble the complex tissue-level HES5 dynamics. Finally, we predict that such dynamic patterning spreads out differentiation events in space, complementing our previous findings whereby the local synchronization controls the rate of differentiation.
Dynamic Phosphorylation Regulates Eukaryotic Translation Initiation Factor 4A Activity During the Cell Cycle
Authors: Sahoo Ansuman , Zollo Robert A. , Shen Shichen , Ashraf Marium , Nelson Samantha , Koudelka Gerald , Qu Jun , Barbi Joseph , Walker Sarah E.
Published: August 2022

The eukaryotic translation initiation factor 4A (eIF4A) resolves mRNA structures to support protein synthesis, yet little is known about its regulation. Here we analyzed eIF4A phosphorylation during alternate stages of the cell cycle, and found three residues near the DEAD box motif (T73, T146, and S177) underwent substantial phosphorylation changes. Phosphomimetic mutations T73D and T146D led to G2/M phase arrest, and abolished eIF4A interaction with RNA, suggesting eIF4A activity is needed for completion of cell division. In addition to these repressive events, we found that S177, a site immediately adjacent to the DEAD-box, showed diametrically opposed phosphorylation, with only phosphorylated S177 present during G1/S arrest and dephosphorylated S177 peptides during G2/M arrest. Phosphomimetic S177D eIF4A increased polysome levels and enhanced normally reduced eIF4A-eIF4G-interaction during G2/M, while phosphodeficient S177A decreased polysome levels and reduced growth, suggesting phosphorylation of S177 enhances eIF4A-mediated translation during G1/S. Together these results suggest that dynamic phosphorylation of eIF4A S177 serves to stimulate translation during G1/S, while inhibitory phosphorylation of additional sites holds the potential to rapidly transition eIF4A to an inactive state and turn off translation. These results also suggest an important role for eIF4A in coupling translation to cell cycle stages.
Haplogenome assembly reveals interspecific structural variation in Eucalyptus hybrids
Authors: Lötter Anneri , Duong Tuan A. , Candotti Julia , Mizrachi Eshchar , Wegrzyn Jill L. , Myburg Alexander A.
Published: August 2022

De novo phased (haplo)genome assembly using long-read DNA sequencing data has improved the detection and characterization of structural variants (SVs) in plant and animal genomes. Able to span across haplotypes, long reads allow phased, haplogenome assembly in highly outbred organisms such as forest trees. Eucalyptus tree species and interspecific hybrids are the most widely planted hardwood trees with F1 hybrids of Eucalyptus grandis and E. urophylla forming the bulk of fast-growing pulpwood plantations in subtropical regions. The extent of structural variation and its effect on interspecific hybridization is unknown in these trees. As a first step towards elucidating the extent of structural variation between the genomes of E. grandis and E. urophylla, we sequenced and assembled the haplogenomes contained in an F1 hybrid of the two species. Using Nanopore sequencing and a trio-binning approach, we assembled the separate haplogenomes (567 Mb and 545 Mb) to 98.8% BUSCO completion. High-density SNP genetic linkage maps of both parents allowed scaffolding of 88% of the haplogenome contigs into 11 pseudo-chromosomes (scaffold N50 of 43.82 Mb and 42.45 Mb for the E. grandis and E. urophylla haplogenomes, respectively). We identify 48,729 SVs between the two haplogenomes providing the first detailed insight into genome structural rearrangement in these species. The two haplogenomes have similar gene content, 35,572 and 33,915 functionally annotated genes, of which 34% are contained in genome rearrangements. Knowledge of SV and haplotype diversity in the two species will form the basis for understanding the genetic basis of hybrid superiority in these trees.

Significance statement

We have produced phased, haplogenome assemblies of an interspecific F1 hybrid using a trio-binning approach and performed the first genome-wide analysis of genome synteny between a subtropical Eucalyptus tree species, E. grandis, and a tropical eucalypt, E. urophylla. This revealed a large number of previously undescribed genome structural variants as a step towards understanding genome structural evolution in this iconic genus of fast-growing woody perennials.
mNGS Investigation of Single Ixodes pacificus Ticks Reveals Diverse Microbes, Viruses, and a Novel mRNA-like Endogenous Viral Elements
Authors: Martyn Calla , Hayes Beth M. , Lauko Domokos , Mithun Edward , Castañeda Gloria , Bosco-Lauth Angela , Kistler Amy , Pollard Katherine S. , Chou Seemay
Published: August 2022

Ticks are increasingly important vectors of human and agricultural diseases. While many studies have focused on tick-borne bacteria, far less is known about tick-associated viruses and their roles in public health or tick physiology. To address this, we investigated patterns of bacterial and viral communities across two field populations of western black-legged ticks (Ixodes pacificus). Through metatranscriptomic analysis of 100 individual ticks, we quantified taxon prevalence, abundance, and co-occurrence with other members of the tick microbiome. Our analysis revealed 11 novel RNA viruses from Rhabdoviridae, Chuviridae, Picornaviridae, Phenuiviridae, Reoviridae, Solemovidiae, Narnaviridae, and 2 highly divergent RNA viruses lacking sequence similarity to known viral families. The majority of these viruses were also detectable in lab-raised ticks at all developmental life stages, localize to tick salivary glands, and show evidence of circulation in mice fed on by ticks. These data suggest that viruses are stable, heritable, and transmissible members of the tick microbiota. We also unexpectedly identified numerous virus-like transcripts that are associated with tick genomic DNA, most of which are distinct from known endogenous viral element-mediated immunity pathways in invertebrates. Together, our work reveals that in addition to potentially serving as vectors for potential viral pathogens, I. pacificus ticks may also have symbiotic partnerships with their own vertically-transmitted viruses or with ancient viruses through evolutionarily acquired virus-like transcripts. Our findings highlight how pervasive and intimate tick–virus interactions are, with major implications for both the fundamental physiology and vector biology of I. pacificus ticks.
Purification of Human β- and γ-actin from Budding Yeast
Authors: Haarer Brian K. , Pimm Morgan L. , de Jong Ebbing P. , Amberg David C. , Henty-Ridilla Jessica L.
Published: August 2022

Biochemical studies of human actin and its binding partners rely heavily on abundant and easily purified α-actin from skeletal muscle. Therefore, muscle actin has been used to evaluate and determine the activities of most actin regulatory proteins and there is an underlying concern that these proteins perform differently with actin present in non-muscle cells. To provide easily accessible and relatively abundant sources of human β- or γ-actin (i.e., cytoplasmic actins), we developedSaccharomyces cerevisiaestrains that express each as their sole source of actin. Both β- or γ-actin purified in this system polymerize and interact with various binding partners, including profilin, mDia1 (formin), fascin, and thymosin-β4 (Tβ4). Notably, Tβ4 and profilin bind to β- or γ-actin with higher affinity than to α-actin, emphasizing the value of testing actin ligands with specific actin isoforms. These reagents will make specific isoforms of actin more accessible for future studies of actin regulation.
Cryo-EM structure of the RADAR supramolecular anti-phage defense complex
Authors: Duncan-Lowey Brianna , Tal Nitzan , Johnson Alex G. , Rawson Shaun , Mayer Megan L. , Doron Shany , Millman Adi , Melamed Sarah , Fedorenko Taya , Kacen Assaf , Amitai Gil , Sorek Rotem , Kranzusch Philip J.
Published: August 2022

RADAR is a two-protein bacterial defense system which was reported to defend against phage by ‘editing’ messenger RNA. Here we determine cryo-EM structures of the RADAR defense complex, revealing RdrA as a heptameric, two-layered AAA+ ATPase and RdrB as a dodecameric, hollow complex with twelve surface-exposed deaminase active sites. RdrA and RdrB join to form a giant assembly up to 10 MDa, with RdrA docked as a funnel over the RdrB active site. Surprisingly, our structures reveal a RdrB active site that targets mononucleotides, not RNA. We show that RdrB catalyzes ATP-to-ITP conversion in vitro and induces the accumulation of inosine mononucleotides during phage infection in vivo, limiting phage replication. Our results define ATP mononucleotide deamination as a determinant of RADAR immunity and reveal supramolecular assembly of a nucleotide-modifying machine as a novel mechanism of anti-phage defense.
Perpendicular Shear Stresses Drive Transmural Helical Remodeling in Engineered Human Ventricular Models
Authors: Williams Nisa P. , Beussman Kevin M. , Foster John R. , Rhodehamel Marcus , Williams Charles A. , Tsui Jonathan H. , Smith Alec S.T. , Mack David L. , Murry Charles E. , Sniadecki Nathan J. , Kim Deok-Ho
Published: August 2022

Tissue engineering with human induced pluripotent stem cell-derived cardiomyocytes enables unique opportunities for creating physiological models of the heart in vitro. However, there are few approaches available that can recapitulate the complex structure-function relationships that govern cardiac function at the macroscopic organ level. Here, we report a down-scaled, conical human 3D ventricular model with controllable cellular organization using multilayered, patterned cardiac sheets. Tissue engineered ventricles whose cardiomyocytes were pre-aligned parallel or perpendicular to the long axis outperformed those whose cardiomyocytes were angled or randomly oriented. Notably, the inner layers of perpendicular cardiac sheets realigned over 4 days into a parallel orientation, creating a helical transmural architecture, whereas minimal remodeling occurred in the parallel or angled sheets. Finite element analysis of engineered ventricles demonstrated that circumferential alignment leads to maximal perpendicular shear stress at the inner layer, whereas longitudinal orientation leads to maximal parallel stress. We hypothesize that cellular remodeling occurs to reduce perpendicular shear stresses in myocardium. This advanced platform provides evidence that physical forces such as shear stress drive self-organization of cardiac architecture.
MDC1 counteracts restrained replication fork restart and its loss causes chemoresistance in BRCA1/2-deficient mammary tumors
Authors: Liptay Martin , Barbosa Joana S. , Gogola Ewa , Duarte Alexandra A. , Dibitetto Diego , Schmid Jonas A. , Klebic Ismar , Mutlu Merve , Siffert Myriam , Francica Paola , Salguero Israel , van de Ven Marieke , Korte-Grimmerink Renske de , Jackson Stephen P. , Jonkers Jos , Lopes Massimo , Rottenberg Sven
Published: August 2022

MDC1 is a key protein in DNA damage signaling. When DNA double-strand breaks (DSBs) occur, MDC1 localizes to sites of damage to promote the recruitment of other factors, including the 53BP1-mediated DSB repair pathway. By studying mechanisms of poly(ADP-ribose) polymerase inhibitor (PARPi) resistance in BRCA2;p53-deficient mouse mammary tumors, we identified a thus far unknown role of MDC1 in replication fork biology. MDC1 localizes at active replication forks during normal fork replication and its loss reduces fork speed. We show that MDC1 contributes to the restart of replication forks and thereby promotes sensitivity to PARPi and cisplatin. Loss of MDC1 causes MRE11-mediated resection, resulting in delayed fork restart. This improves DNA damage tolerance and causes chemoresistance in BRCA1/2-deficient cells. Hence, our results show a role for MDC1 in replication fork progression that mediates PARPi- and cisplatin-induced DNA damage, in addition to its role in DSB repair.
Autologous humanized PDX modeling for immuno-oncology recapitulates the human tumor microenvironment
Authors: Chiorazzi Michael , Martinek Jan , Krasnick Bradley , Zheng Yunjiang , Robbins Keenan J , Qu Rihao , Kaufmann Gabriel , Skidmore Zachary , Henze Laura A , Brösecke Frederic , Adonyi Adam , Zhao Jun , Shan Liang , Sefik Esen , Mudd Jacqueline , Bi Ye , Goedegebuure S Peter , Griffith Malachi , Griffith Obi , Oyedeji Abimbola , Fertuzinhos Sofia , Garcia-Milian Rolando , Boffa Daniel , Detterbeck Frank , Dhanasopon Andrew , Blasberg Justin , Judson Benjamin , Gettinger Scott , Politi Katerina , Kluger Yuval , Palucka A Karolina , Fields Ryan , Flavell Richard A
Published: August 2022

Interactions between immune and tumor cells are critical to determining cancer progression and response. In addition, preclinical prediction of immune-related drug efficacy is limited by inter-species differences between human and mouse, as well as inter-person germline and somatic variation. Here we develop an autologous system that models the TME in individual patients. With patient-derived bone marrow, we engrafted a patient’s hematopoietic system in MISTRG6 mice followed by patient-derived xenograft (PDX) tissue, providing a genetically matched autologous model. We used this system to prospectively study tumor-immune interactions in solid tumor patients. Autologous PDX mice generated innate and adaptive immune populations; these cells populated the TME; and tumors from autologously engrafted mice grew larger than tumors from non-engrafted littermate controls. Single-cell transcriptomics revealed a prominent VEGF-A signature in TME myeloid cells, and inhibition of human VEGF-A abrogated enhanced growth, demonstrating the utility of the autologous PDX system for pre-clinical testing.
Group AStreptococcusantibiotic tolerance in necrotizing fasciitis
Authors: Keller Nadia , Boumasmoud Mathilde , Andreoni Federica , Tarnutzer Andrea , von Matt Manuela , Scheier Thomas C. , Gómez-Mejia Alejandro , Huemer Markus , Marques-Maggio Ewerton , Schuepbach Reto A. , Mairpady-Shambat Srikanth , Brugger Silvio D. , Zinkernagel Annelies S.
Published: August 2022

Objectives

Group AStreptococcus(GAS) necrotizing fasciitis (NF) is a difficult-to-treat bacterial infection associated with high morbidity and mortality despite extensive surgery and targeted antibiotic treatment. Bacteria surviving prolonged antibiotic exposure without displaying genetic resistance, so-called persisters, are associated with difficult-to-treat infections, such as GAS-NF. In the present study, we investigated the presence of persistent GAS in tissue freshly debrided from three NF patients and examined more in depth the persisters phenomenon in GAS-NF clinical isolates.

Methods

Time-lapse imaging of freshly isolated GAS-NF clinical isolates, the image analysis software ColTapp and antibiotic challenge-based persisters assays were used to assess the presence of persisters.

Results

We show for the first time that GAS recovered directly from freshly debrided NF patient’s tissue are characterized by increased colony appearance time heterogeneity, indicating the presence of persisters. Acidic pH or nutrient stress exposure, mimicking the NF-like environment in vitro, similarly leads to phenotypic heterogeneity resulting in enhanced antibiotic survival and confirming the presence of GAS persisters.

Conclusions

GAS persisters are present in the tissue freshly debrided from GAS-NF patients and might be one explanation for antibiotic treatment failure and surgery requirement in GAS-NF. Tailored treatment options, including the use of persisters-targeting drugs, need to be developed to increase GAS-NF therapy success.
A continuous epistasis model for predicting growth rate given combinatorial variation in gene expression and environment
Authors: Otto Ryan M. , Turska-Nowak Agata , Brown Philip M. , Reynolds Kimberly A.
Published: August 2022

The ability to predict changes in cellular growth rate given variation in gene expression is critical to engineer biosynthetic pathways and understand evolutionary constraints on mRNA abundance. However, the relationship between gene expression and growth rate is nonlinear and shaped by environmental and genetic context. To address these challenges, we examined the relationship between enzyme expression andE. coligrowth rate for 36 metabolic gene pairs by measuring growth following 4,404 pairwise, titrated changes in enzyme abundance under varied environmental contexts. Using 20% of these data, we trained an interpretable epistatic model to predict growth rate following simultaneous expression and environmental perturbations. The model’s predictions were robust to significant genetic and environmental epistasis and at times approached the accuracy of biological replicates. Based on these results, we propose a strategy using sparsely sampled, low-order measurements to quantify genetic interaction landscapes on the pathway-wide or genomic scale in a single assay.
Paternal methamphetamine exposure induces higher sensitivity to methamphetamine in male offspring through driving ADRB1 on CaMKII-positive neurons in mPFC
Authors: Zheng Yanyan , Liu Dekang , Guo Hao , Chen Wenwen , Liu Zhaoyu , Li Zhaosu , Hu Tao , Zhang Yuanyuan , Li Xiang , Zhao Ziheng , Cai Qinglong , Ge Feifei , Fan Yu , Guan Xiaowei
Published: August 2022

Paternal abuse of drugs, such as methamphetamine (METH), elevates the risk of developing addiction in subsequent generations, however, its underlying molecular mechanism remains poorly understood. Male adult mice (F0) were exposed to METH for 30 days, followed by mating with naïve female mice to create the first-generation mice (F1). When growing to adulthood, F1 were subjected to conditioned place preference (CPP) test. Subthreshold dose of METH, insufficient to induce CPP normally, were used in F1 (METHF1). Selective antagonist (betaxolol) for β1-adrenergic receptor (ADRB1) or its knocking-down virus were administrated into mPFC to regulate ADRB1 function and expression on CaMKII-positive neurons. METH-sired male F1 acquired METHF1-induced CPP, indicating that paternal METH exposure induce higher sensitivity to METH in male F1. Compared with saline (SAL)-sired male F1, CaMKII-positive neuronal activity was normal without METHF1, but strongly evoked after METHF1treatment in METH-sired male F1 during adulthood. METH-sired male F1 had higher ADRB1 levels without METHF1, which was kept at higher levels after METHF1treatment in mPFC. Either inhibiting ADRB1 function with betaxolol, or knocking-down ADRB1 level on CaMKII-positive neurons (ADRB1CaMKII) with virus transfection efficiently suppressed METHF1-evoked mPFC acyivation, and ultimately blocked METHF1-induced CPP in METH-sired male F1. In the process, the p-ERK1/2 and ΔFosB may be potential subsequent signals of mPFC ADRB1CaMKII. The mPFC ADRB1CaMKIImediates paternal METH exposure-induced higher sensitivity to drug addiction in male offspring, raising a promising pharmacological target for predicting or treating transgenerational addiction.

HIGHLIGHTS

Paternal methamphetamine (METH) exposure induces higher sensitivity to METH in male F1 during adulthood, accompanied with higher ADRB1 level in mPFC.

METH use in F1 (METHF1) evokes more CaMKII-positive neurons in mPFC of METH-sired than saline-sired male F1.

Inhibiting ADRB1 function or knocking-down ADRB1 level on CaMKII-positive neurons (ADRB1CaMKII) efficiently suppresses METHF1-evoked mPFC activation, and ultimately rescues transgenerational susceptibility to addiction in male F1.
Sex differences in the impact of electronic nicotine vapor on corticotropin-releasing factor receptor 1 neurons in the mouse ventral tegmental area
Authors: Zhu ManHua , Rogers Neil G , Jahad Jasmine V , Herman Melissa A
Published: August 2022

Nicotine engages dopamine neurons in the ventral tegmental area (VTA) to encode reward and drive the development of nicotine addiction, however how nicotine selectively alters other VTA populations remains to be determined. Here, we used male and female CRF1-GFP mice and nicotine vapor exposure to examine the effects of nicotine in VTA corticotropin-releasing factor receptor 1 (CRF1) neurons. We use immunohistochemistry and electrophysiology to examine neuronal activity, excitability, and inhibitory signaling. We found that VTA CRF1 neurons are mainly dopaminergic and project to the nucleus accumbens (VTA-NAcCRF1 neurons).VTA-NAcCRF1 neurons show greater phasic inhibition in naïve females and greater focal nicotine-induced increases in firing in naïve males. Following acute nicotine vapor exposure, phasic inhibition was not altered, but focal nicotine-induced tonic inhibition was enhanced in females and diminished in males. Acute nicotine vapor exposure did not affect firing inVTA-NAcCRF1 neurons, but females showed lower baseline firing and higher focal nicotine-induced firing. Activity (cFos) was increased in the CRF1 dopaminergic VTA population in both sexes, but with greater increases in females. Following chronic nicotine vapor exposure, both sexes displayed reduced basal phasic inhibition and the sex difference in tonic inhibition following acute vapor exposure was no longer observed. Additionally, activity of the CRF1 dopaminergic VTA population was no longer elevated in either sex. These findings reveal sex- and exposure-dependent changes in mesolimbic VTA-NAc CRF1 neuronal activity, inhibitory signaling, and nicotine sensitivity following nicotine vapor exposure. These changes potentially contribute to nicotine-dependent behaviors and the intersection between stress, anxiety, and addiction.