bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome Sequence Resource of Serratia ureilytica HNU47: A Strain with Biocontrol Potential Against Bacterial Wilt Pathogen Ralstonia solanacearum
Authors: Cao Xiulan , Ye Yuting , Li Peng
Published: October 2022

Serratia ureilytica HNU47 was originally isolated from rhizosphere soil of stock in a continuous cropping tomato-planting field, which has excellent antagonistic ability against Ralstonia solanacearum. Here, we sequenced the genome of HNU47 to gain insights into the underlying basis of its antagonistic activity. Results of phylogenetic analysis of the whole genomic sequence demonstrated that HNU47 belongs to S. ureilytica. Through antiSMASH analysis, 10 secondary metabolite biosynthesis gene clusters were predicted. There were only two gene clusters with similarity higher than 95% with known compounds’ gene clusters and the similarities of the other eight gene clusters were lower than 30%, including three gene clusters with no homology. In addition, biocontrol experiments confirmed that HNU47 could decrease the incidence of bacterial wilt caused by R. solanacearum on tomato. These findings support the potential of developing S. ureilytica HNU47 as a biocontrol agent against R. solanacearum by producing some unknown active compounds. The genome sequence reported here is also useful for revealing the modulation mechanisms underlying biosynthesis of active compounds.
Ozone Therapy in the Comprehensive Treatment of Leg Ulcers: Case Report
Authors: Pasek Jarosław , Stanek Agata , Szyluk Karol , Cieślar Grzegorz
Published: October 2022

Treatment with ozone therapy is of interest in many fields of medicine. In the field of angiology, ozone is used to treat infected wounds that are difficult to heal. In this case report, the authors report the introduction of innovative therapeutic equipment into clinical practice to accelerate the healing process of clinical wounds by the external application of ozone in various forms. They present positive results of the comprehensive treatment of a 52-year-old woman with an ulcer on her right lower leg, which formed after a previous orthopedic surgery. In addition to pharmacotherapy and compression therapy, local ozone therapy was applied. After 30 ozone therapy procedures, the ulcer healed completely, and the patient’s pain was significantly alleviated, as assessed by a visual analog scale (9.0 points before therapy vs 0.5 point after therapy). As a result, the patient’s quality of life improved, as assessed by the EuroQol scale (10 points before therapy vs 90 points after therapy).

The use of local ozone therapy can be an appropriate complement in the comprehensive treatment of chronic wounds. In the presented case, ozone therapy helped complete healing of the ulcer and significantly reduced the intensity of pain experienced, thus improving the patient’s quality of life.
Does Sacrococcygeal Skeletal Morphology and Morphometry Influence Pressure Injury Formation in Adults?
Authors: Delmore Barbara , Sprigle Stephen , Samim Mohammad , Alfonso Allyson R. , Lin Lawrence , Chiu Ernest
Published: October 2022

GENERAL PURPOSE

To present a study that investigated sacrococcygeal skeletal structure as a possible nonmodifiable intrinsic risk factor for pressure injury and identify possible issues caused by its morphology.

TARGET AUDIENCE

This continuing education activity is intended for physicians, physician assistants, nurse practitioners, and nurses with an interest in skin and wound care.

LEARNING OBJECTIVES/OUTCOMES

After participating in this educational activity, the participant will:

1. Recognize the background information the authors considered when planning and conducting their study of sacrococcygeal skeletal structure as a possible pressure injury risk factor.

2. Identify the characteristics of the two groups of study participants.

3. Choose the results of the study clinicians may consider when implementing evidence-based practice.

Objective

To determine if sacrococcygeal skeletal morphology and morphometry characteristics were possible pressure injury (PI) intrinsic risk factors; determine the exact location of these PIs; and generate hypotheses and determine methodological considerations required for future larger studies.

Methods

This case-control pilot study compared 30 patients who had an MRI scan—15 patients had a PI and 15 patients did not. Key sacrococcygeal morphology and morphometry parameters were assessed.

Results

On average, patients with PIs had less of a lumbosacral and sacrococcygeal angle and a greater sacral curvature and intercoccygeal angle than did patients without a PI. Patients with PIs had more variable coccyx types. Tissue and bone destruction precluded several measurements in some patients. The most common area of destruction was located distally.

Conclusion

Sacrococcygeal measurements differed in patients with PIs, and PIs were predominately located distally. Authors recommend replicating this study on a larger scale because certain key attributes warrant further investigation to determine their influence on sacrococcygeal PIs. Sacrococcygeal morphology and morphometry parameters have not been previously studied as possible intrinsic risk factors for PIs; yet, this is the most common location for their occurrence. Knowledge regarding possible injury mechanisms due to the forces from overlying skeletal structures with respective tissue loading over the sacrococcygeal area has the potential to inform practice; preventive strategies; and equipment, products, and technology developed.
A Polio Epidemic Is Averted
Authors: Todd Betsy
Published: October 2022

Editor's note: From its first issue in 1900 through to the present day, AJN has unparalleled archives detailing nurses' work and lives over more than a century. These articles not only chronicle nursing's growth as a profession within the context of the events of the day, but also reveal prevailing societal attitudes about women, health care, and human rights. Today's nursing school curricula rarely include nursing's history, but it's a history worth knowing. To this end, From the AJN Archives highlights articles selected to fit today's topics and times.

In August 1961, the incidence of polio was rising in and around Syracuse, New York, and oral polio vaccine had just been made available. In this article from AJN's May 1962 issue, Syracuse Department of Health director of nursing Alyce Rooney details the rapid planning that resulted in the administration of more than 400,000 polio vaccines over a period of just three days.

In an incredible effort over less than two weeks, vaccine was obtained and repackaged, vaccination sites were secured, staff assignments were made, and the vaccines were given. After a high of 46 Syracuse-area polio cases in August, the number dropped to 18 in September and none in October.

More than 50 years later, vaccine hesitancy has become a roadblock to today's vaccination campaigns. In this issue, research by Roberts and colleagues provides an understanding of vaccine hesitancy among nurses, which may inform the development of policies, campaigns, and interventions aimed at increasing nurse vaccination rates.—Betsy Todd, MPH, RN
A Case of a Man with Syncope After Physical Exertion
Authors: Kupchik Nicole , Green Joel
Published: October 2022

Editor's note: This is the next installment in a series on electrocardiogram (ECG) interpretation. Nurses in all settings should know the basics, as medications and physiological changes can cause cardiac arrhythmias. Each article will start with a brief case scenario and an ECG strip and then take you step by step through analyzing the heart rhythm.
The Trauma and Grief of Frontline Clinicians
Authors: Brown Theresa
Published: October 2022

A journalist investigates and offers a way forward.
Time as Friend and Foe
Authors: Stathis Courtney
Published: October 2022

Pondering time's ubiquitous role in health care and the rest of life.
The nurse's quick guide to I.V. drug calculations
Authors: Wilson Kelley Miller , Wilson Elizabeth Megan
Published: October 2022

Nurses must become proficient with complex calculations that occur in everyday practice. This case study approach provides insight and practice of common calculations.
Serial Measurements of Protein Biomarkers in Sepsis-Induced Acute Respiratory Distress Syndrome
Authors: Yang Philip , Iffrig Elizabeth , Harris Frank , Holder Andre L. , Martin Greg S. , Esper Annette M.
Published: October 2022

IMPORTANCE:

The role of early, serial measurements of protein biomarkers in sepsis-induced acute respiratory distress syndrome (ARDS) is not clear.

OBJECTIVES:

To determine the differences in soluble receptor for advanced glycation end-products (sRAGEs), angiopoietin-2, and surfactant protein-D (SP-D) levels and their changes over time between sepsis patients with and without ARDS.

DESIGN, SETTING, AND PARTICIPANTS:

Prospective observational cohort study of adult patients admitted to the medical ICU at Grady Memorial Hospital within 72 hours of sepsis diagnosis.

MAIN OUTCOMES AND MEASURES:

Plasma sRAGE, angiopoietin-2, and SP-D levels were measured for 3 consecutive days after enrollment. The primary outcome was ARDS development, and the secondary outcome of 28-day mortality. The biomarker levels and their changes over time were compared between ARDS and non-ARDS patients and between nonsurvivors and survivors.

RESULTS:

We enrolled 111 patients, and 21 patients (18.9%) developed ARDS. The three biomarker levels were not significantly different between ARDS and non-ARDS patients on all 3 days of measurement. Nonsurvivors had higher levels of all three biomarkers than did survivors on multiple days. The changes of the biomarker levels over time were not different between the outcome groups. Logistic regression analyses showed association between day 1 SP-D level and mortality (odds ratio, 1.52; 95% CI, 1.03–2.24; p = 0.03), and generalized estimating equation analyses showed association between angiopoietin-2 levels and mortality (estimate 0.0002; se 0.0001; p = 0.04).

CONCLUSIONS AND RELEVANCE:

Among critically ill patients with sepsis, sRAGE, angiopoietin-2, and SP-D levels were not significantly different between ARDS and non-ARDS patients but were higher in nonsurvivors compared with survivors. The trend toward higher levels of sRAGE and SP-D, but not of angiopoietin-2, in ARDS patients may indicate the importance of epithelial injury in sepsis-induced ARDS. Changes of the biomarker levels over time were not different between the outcome groups.
It’s not all about the MIC: Daptomycin synergy with β-lactams varies between enterococcal species where cardiolipin synthase mutations confer daptomycin resistance
Authors: McKew Genevieve
Published: October 2022

Introduction

Administering daptomycin with β-lactams may prevent resistance or achieve synergy in enterococcal infections. Daptomycin-non-susceptibility (DAP-NS) phenotype is commonly associated with mutations in the liaFSR and YycFGHIJ systems. Cardiolipin synthase (cls) mutations have been found in conjunction with liaFSR mutations, associated with higher MICs, suggesting they are stepwise mutations. In vitro, ampicillin restores daptomycin bactericidal activity in Enterococcus faecium isolates with liaFSR mutations, but not when they occur in the cls gene; cls-only Enterococcus faecalis mutants have not yet been reported.

Aim

The aim was to explore daptomycin synergy with β-lactams for high-MIC DAP-NS E. faecalis and E. faecium cls mutants.

Methodology

Experimentally-induced DAP-NS E. faecalis (A7) and DAP-NS E. faecium (C_002) from a persistent infection on daptomycin-ampicillin therapy had whole-genome sequencing (AB SOLiD 5500, CLC Genomics Workbench 9). Time-kill studies were performed with DAP, ampicillin, and DAP-AMP; and ceftriaxone and DAP-ceftriaxone for E. faecalis.

Results

Both isolates’ only DAP-NS-associated mutation was in cls. DAP-ceftriaxone demonstrated bactericidal activity and synergy for E. faecalis A7, whereas E. faecium C_002 grew in the presence of DAP and DAP-AMP.

Conclusion

High-level DAP-NS arose in association with a cls mutation alone in E. faecalis A7, and in the absence of other documented DAP-NS-associated genetic mutations in E. faecium C_002. DAP-ceftriaxone combination therapy may be a useful salvage option in DAP-NS E. faecalis infections carrying the cls mutation identified in this study. There was no in vitro DAP-ampicillin synergy for cls-associated DAP-NS E. faecium C_002.
Qualitative Determination of Bioactive Metabolites of Chyawanprash by Using Gas Chromatography-Mass Spectroscopy
Authors: Rajesh Babu K , Saleem T S M , Thiruvengada Rajan V S , Madhu M , Chand Basha S , Narasimhulu U
Published: October 2022

Chyawanprash is a rich source of all the major bioactive metabolites because of its authentic and natural composition and widely used due to its medicinal properties. In the present study, the precise flow of analytical methods was employed for the identification and characterization of unknown secondary metabolites in Chyawanprash. The phytochemical components of the whole formulation were extracted using n-hexane, ethyl acetate, and methanol by maceration which shows the presence of all the major secondary metabolite components through preliminary qualitative phytochemical screening. The GC-MS analysis of different extracts of Chyawanprash was investigated using Clarus 680 GC (Perkin-Elmer (U. S. A) 30 m X 0.25 mm ID X 250 μm DF) which revealed the presence of total 15 unknown secondary metabolites. Finally, the results showed that the study forms the basis for the phytochemical characterization of Chyawanprash extracts, the isolation of responsible bio-active metabolites and their biological activity is necessary for future studies.
An Investigation of the Effects of Nitrate vs. Ammonium on Plants Using Metabolic Modeling
Authors: Lai Iris , Maurice Cheung C. Y.
Published: October 2022

As metabolism is a very complex process, it is essential to use computational modeling to better understand the changes in metabolism at a systems level. In this paper, we used a computational model that simulates the metabolism of mature plants to test how the use of nitrate and ammonium as nitrogen sources affects plant metabolism. Our model predicted and showed the possible changes in metabolism in different plant tissues in response to the use of different nitrogen sources. Our methodology produces predictions of metabolic fluxes in plants and improves our understanding of how plants react to changes in conditions. This research can potentially give insights into how we can improve crop yield by identifying metabolic processes that are important in plant growth and in the adaptation to different nitrogen sources. In future research work, we can apply the existing model to explore the effects of different nutrient availability under different conditions (e.g. well-watered vs drought) to optimize nutrient availability under particular environmental conditions. Experimental researchers, plant breeders, and farmers can use the knowledge gained from the modeling work to further our understanding of plant metabolism and apply the knowledge to improve plant growth in the lab and the field.
Emergence of linkage between cooperative RNA replicators encoding replication and metabolic enzymes thorough experimental evolution
Authors: Ueda Kensuke , Mizuuchi Ryo , Ichihashi Norikazu
Published: October 2022

The integration of individually replicating genes into a primitive chromosome is a key evolutionary transition in the development of life, allowing the simultaneous inheritance of genes. However, how this transition occurred is unclear because of the extended size of primitive chromosomes, which replicate slower than unlinked genes. Theoretical studies have suggested that a primitive chromosome can evolve in the presence of cell-like compartments, as the physical linkage prevents the stochastic loss of essential genes upon division, but experimental support for this is lacking. Here, we demonstrate the evolution of a chromosome-like RNA from two cooperative RNA replicators encoding replication and metabolic enzymes. Through their long-term replication in cell-like compartments, linked RNAs emerged with the two cooperative RNAs connected end-to-end. The linked RNAs had different mutation patterns than the two unlinked RNAs, suggesting that they were maintained as partially distinct lineages in the population. Our results provide experimental evidence supporting the plausibility of the evolution of a primitive chromosome from unlinked gene fragments, an important step in the emergence of complex biological systems.

Author Summary

The integration of genes into a chromosome is a fundamental genetic organization in all extant life. The assembly of unlinked genes during prebiotic evolution was likely a major evolutionary transition toward the development of a complex cell. Decades of theoretical studies have suggested a plausible evolutionary pathway to a primitive chromosome from replicating RNA molecules that harbor cooperative genes within a protocell structure. However, demonstrating the evolution of a primitive chromosome in an experimental setup is challenging. We previously developed a cooperative RNA replication system in which two types of RNAs co-replicate using their self-encoded replication and metabolic enzymes. Using this system, in the present study, we demonstrate the evolution of a linkage between the two cooperative RNA replicators in compartments. An evolved “linked” RNA harbored the entire region of both genes, accumulated distinct mutations, and retained the ability to replicate using the two proteins translated from itself. These experimental findings support a prebiotic evolutionary scenario, in which unlinked genes assembled into a single genomic structure.
Full-length merozoite surface protein 1 ofPlasmodium falciparumis a major target of protective immunity following controlled human malaria infections
Authors: Rosenkranz Micha , Nkumama Irene N. , Kraker Sara , Blickling Marie , Mwai Kennedy , Odera Dennis , Tuju James , Fürle Kristin , Frank Roland , Chepsat Emily , Kapulu Melissa C. ,   CHMI-SIKA study team, Osier Faith H. A.
Published: October 2022

The merozoite surface protein 1 (MSP1) is the most abundant protein on the surface of the invasive merozoite stages ofPlasmodium falciparumand has long been considered a key target of protective immunity. However, previous studies focused on small C-terminal fragments and potentially missed the opportunity to identify important epitopes that are relevant for protection. We used samples from a controlled human malaria challenge (CHMI) study in semi-immune volunteers to show that levels of pre-challenge antibodies directed against the full-length MSP1 (MSP1FL) are significantly correlated with protection from malaria. Furthermore, we showed that anti-MSP1FLantibodies induced five distinct Fc-mediated effector mechanisms: complement fixation, phagocytosis, respiratory burst, degranulation and IFNγ production, each of which was strongly associated with protection. The breadth of Fc-mediated effector functions was the strongest correlate of protection. Our findings suggest that MSP1FLis an important target of functional antibodies that contribute to a protective immune response against malaria and support the development of MSP1FL-based vaccines.
Bioacoustic Event Detection with Self-Supervised Contrastive Learning
Authors: Bermant Peter C. , Brickson Leandra , Titus Alexander J.
Published: October 2022

While deep learning has revolutionized ecological data analysis, existing strategies often rely on supervised learning, which is subject to limitations on real-world applicability. In this paper, we apply self-supervised deep learning methods to bioacoustic data to enable unsupervised detection of bioacoustic event boundaries. We propose a convolutional deep neural network that operates on the raw waveform directly and is trained in accordance with the Noise Contrastive Estimation principle, which enables the system to detect spectral changes in the input acoustic stream. The model learns a representation of the input audio sampled at low frequency that encodes information regarding dissimilarity between sequential acoustic windows. During inference, we use a peak finding algorithm to search for regions of high dissimilarity in order to identify temporal boundaries of bioacoustic events. We report results using these techniques to detect sperm whale (Physeter macrocephalus) coda clicks in real-world recordings, and we demonstrate the viability of analyzing the vocalizations of other species (e.g. Bengalese finch syllable segmentation) in addition to other data modalities (e.g. animal behavioral dynamics, embryo development and tracking). We find that the self-supervised deep representation learning-based technique outperforms established threshold-based baseline methods without requiring manual annotation of acoustic datasets. Quantitatively, our approach yields a maximal R-value and F1-score of 0.887 and 0.876, respectively, and an area under the Precision-Recall curve (PR-AUC) of 0.917, while a baseline threshold detector acting on signal energy amplitude returns a maximal R-value and F1-score of 0.620 and 0.576, respectively, and a PR-AUC of 0.571. We also compare with a threshold detector using preprocessed (e.g. denoised) acoustic input. The findings of this paper establish the validity of unsupervised bioacoustic event detection using deep neural networks and self-supervised contrastive learning as an effective alternative to conventional techniques that leverage supervised methods for signal presence indication. Providing a means for highly accurate unsupervised detection, this paper serves as an important step towards developing a fully automated system for real-time acoustic monitoring of bioacoustic signals in real-world acoustic data. All code and data used in this study are available online.
Historical dispersal and host-switching formed the evolutionary history of a globally distributed multi-host parasite - theLigula intestinalisspecies complex
Authors: Nazarizadeh Masoud , Nováková Milena , Loot Géraldine , Gabagambi Nestory P. , Fatemizadeh Faezeh , Osano Odipo , Presswell Bronwen , Poulin Robert , Vitál Zoltán , Scholz Tomáš , Halajian Ali , Trucchi Emiliano , Kočová Pavlína , Štefka Jan
Published: October 2022

Studies on parasite biogeography and host spectrum provide insights into the processes driving parasite diversification. Global geographical distribution and a multi-host spectrum make the tapewormLigula intestinalisa promising model for studying both the vicariant and ecological modes of speciation in parasites. To understand the relative importance of host association and biogeography in the evolutionary history of this tapeworm, we analysed mtDNA and reduced-represented genomic SNP data for a total of 139 specimens collected from 18 fish-host genera across a distribution range representing 21 countries. Our results strongly supported the existence of at least 10 evolutionary lineages and estimated the deepest divergence at approximately 4.99-5.05 Mya, which is much younger than the diversification of the fish host genera and orders. Historical biogeography analyses revealed that the ancestor of the parasite diversified following multiple vicariance events and was widespread throughout the Palearctic, Afrotropical, and Nearctic between the late Miocene and early Pliocene. Cyprinoids were inferred as the ancestral hosts for the parasite. Later, from the late Pliocene to Pleistocene, new lineages emerged following a series of biogeographic dispersal and host-switching events. Although only a few of the currentLigulalineages show narrow host-specificity (to a single host genus), almost no host genera, even those that live in sympatry, overlapped between differentLigulalineages. Our analyses uncovered the impact of historical distribution shifts on host switching and the evolution of host specificity without parallel host-parasite co-speciation. Historical biogeography reconstructions also found that the parasite colonized several areas (Afrotropical and Australasian) much earlier than was suggested by only recent faunistic data.
Multi-level Bayesian analysis of monk parakeet contact calls shows dialects between European cities
Authors: Smeele Simeon Q. , Tyndel Stephen A. , Aplin Lucy M. , McElreath Mary Brooke
Published: October 2022

Geographic differences in vocalisations provide strong evidence for animal culture, with patterns likely arising from generations of social learning and transmission. The current knowledge on the evolution of vocal variation has predominantly focused on fixed repertoire, territorial song in passerine birds. The study of vocal communication in open-ended learners and in contexts where vocalisations serve other functions is therefore necessary for a more comprehensive understanding of vocal dialect evolution. Parrots are open-ended vocal production learners that use vocalisations for social contact and coordination. Geographic variation in parrot vocalisations typically take the form of either distinct regional variations known as dialects or graded variation based on geographic distance known as clinal variation. In this study, we recorded monk parakeets (Myiopsitta monachus) across multiple spatial scales (i.e. parks and cities) in their European invasive range. We then compared calls using a multi-level Bayesian model and sensitivity analysis, with this novel approach allowing us to explicitly compare vocalisations at multiple spatial scales. We found support for founder effects and/or cultural drift at the city level, consistent with passive cultural processes leading to large scale dialect differences. We did not find a strong signal for dialect or clinal differences between parks within cities, suggesting that birds did not actively converge on a group level signal, as expected under the group membership hypothesis. We demonstrate the robustness of our findings and offer an explanation that unifies the results of prior monk parakeet vocalisation studies.
VECTRON™ T500, a new broflanilide insecticide for indoor residual spraying, provides prolonged control of pyrethroid-resistant malaria vectors
Authors: Govoetchan Renaud , Fongnikin Augustin , Syme Thomas , Small Graham , Gbegbo Martial , Todjinou Damien , Rowland Mark , Nimmo Derric , Padonou Germain Gil , Ngufor Corine
Published: October 2022

Background

Broflanilide is a newly discovered insecticide with a novel mode of action targeting insect γ-aminobutyric acid receptors. The efficacy of VECTRON™ T500, a wettable powder formulation of broflanilide, was assessed for IRS against wild pyrethroid-resistant malaria vectors in experimental huts in Benin.

Methods

VECTRON™ T500 was evaluated at 100 mg/m² in mud and cement-walled experimental huts against wild pyrethroid-resistantAnopheles gambiae sensu lato(s.l.) in Covè, southern Benin, over 18 months. A direct comparison was made with Actellic® 300CS, a WHO-recommended micro-encapsulated formulation of pirimiphos-methyl, applied at 1000 mg/m². The vector population at Covè was investigated for susceptibility to broflanilide and other classes of insecticides used for vector control. Monthly wall cone bioassays were performed to assess the residual efficacy of VECTRON™ T500 using insecticide susceptibleAn. gambiaeKisumu and pyrethroid-resistantAn. gambiae s.l. Covè strains. The study complied with OECD principles of good laboratory practice.

Results

The vector population at Covè was resistant to pyrethroids and organochlorines but susceptible to broflanilide and pirimiphos-methyl. A total of 23,171 free-flying wild pyrethroid-resistant femaleAn. gambiae s.l. were collected in the experimental huts over 12 months. VECTRON™ T500 induced 56%-60% mortality in wild vector mosquitoes in both cement and mud-walled huts. Mortality with VECTRON™ T500 was 62%-73% in the first three months and remained >50% for 9 months on both substrate-types. By comparison, mortality with Actellic® 300CS was very high in the first three months (72%-95%) but declined sharply to <40% after 4 months. Using a non-inferiority margin defined by the World Health Organization, overall mortality achieved with VECTRON™ T500 was non-inferior to that observed in huts treated with Actellic® 300CS with both cement and mud wall substrates. Monthlyin situwall cone bioassay mortality with VECTRON™ T500 also remained over 80 % for 18 months but dropped below 80% with Actellic® 300CS at 6-7 months post spraying.

Conclusion

VECTRON™ T500 shows potential to provide substantial and prolonged control of malaria transmitted by pyrethroid-resistant mosquito vectors when applied for IRS. Its addition to the current list of WHO-approved IRS insecticides will provide a suitable option to facilitate rotation of IRS products with different modes of action.
FC2 stabilizes POR and suppresses ALA formation in the tetrapyrrole biosynthesis pathway
Authors: Fan Tingting , Roling Lena , Hedtke Boris , Grimm Bernhard
Published: October 2022

During photoperiodic growth, the light-dependent nature of chlorophyll synthesis in angiosperms necessitates robust control of the production of 5-aminolevulinic acid (ALA), the rate-limiting step in the initial stage of tetrapyrrole biosynthesis (TBS). We are interested in dissecting the post-translational control of this process, which suppresses ALA synthesis for chlorophyll synthesis in dark-grown plants.

Using biochemical approaches for analysis of wild-type and mutant lines as well as complementation lines, we show that the heme-synthesizing ferrochelatase 2 (FC2) interacts with protochlorophyllide oxidoreductase and the regulator FLU which both promote the feedback-controlled suppression of ALA synthesis by inactivation of glutamyl-tRNA reductase, thus preventing excessive accumulation of potentially deleterious tetrapyrrole intermediates.

Thereby FC2 stabilizes POR by physical interaction. When the interaction between FC2 and POR is perturbed, suppression of ALA synthesis is attenuated and photoreactive protochlorophyllide accumulates. FC2 is anchored in the thylakoid membrane via its membrane-spanning CAB (chlorophyll-a-binding) domain.

FC2 is one of the two isoforms of ferrochelatase catalyzing the last step of heme synthesis. Although FC2 belongs to the heme-synthesizing branch of TBS, its interaction with POR potentiates the effects of the GluTR-inactivation complex on the chlorophyll-synthesizing branch, and ensures reciprocal control of chlorophyll and heme synthesis.
POU6F2mutation identified in humans with pubertal failure shifts isoform formation and alters GnRH transcript expression
Authors: Cho Hyun-Ju , Gurbuz Fatih , Stamou Maria , Kotan Leman Damla , Farmer Stephen Matthew , Can Sule , Tompkins Miranda Faith , Mammadova Jamala , Altincik S. Ayca , Gokce Cumali , Catli Gonul , Bugrul Fuat , Bartlett Keenan , Turan Ihsan , Balasubramanian Ravikumar , Yuksel Bilgin , Seminara Stephanie B. , Wray Susan , Topaloglu A. Kemal
Published: October 2022

Idiopathic hypogonadotropic hypogonadism (IHH) is characterized by absent pubertal development and infertility, often due to gonadotropin-releasing hormone (GnRH) deficits. Exome sequencing of two independent cohorts of IHH patients identified 12 rare missense variants inPOU6F2. POU6F2encodes two distinct isoforms. In mouse, pituitary and gonads expressed both isoforms, but only isoform1 was detected in GnRH cells. Although the function of isoform2 is well known, using bioinformatics and cells assays on a human-derived GnRH cell line, we demonstrate isoform1 can also act as a transcriptional regulator, decreasingGNRH1expression. The impact of twoPOU6F2variants (MT1 and MT2) was then examined. MT1, but not MT2, reduced transcriptional activity of either isoform, preventing Hes5 promoter activation by isoform2 and repression of GnRH transcripts by isoform1. GnRH transcription increases as the cells migrate into the brain. Augmentation earlier can disrupt normal GnRH cell migration, consistent with POU6F2 variants contributing to IHH pathogenesis.
Epigenetic and transcriptional plasticity drive inflammation in Cystic Fibrosis
Authors: Dinan Adam M. , Eneje Odiri , Brown Karen P. , Burden Frances , Morse Mary , Prinjha Rab K. , Frontini Mattia , Floto R. Andres
Published: October 2022

The relative contributions of acute and chronic inflammatory mechanisms in diseases characterised by persistent bacterial infection are unclear, despite important consequences for the development of novel anti-inflammatory therapies. Here, we examined longitudinal transcriptional and epigenetic changes in patients with Cystic Fibrosis (CF), a genetic condition characterised by persistent bacterial lung infections that drive progressive inflammatory lung damage. We find that sudden clinical deteriorations in lung health, termed Acute Pulmonary Exacerbations (APEs), are linked to innate immune signalling driven by bacterial components, and accompanied by changes in macrophage function. Treatment of patients with intravenous antibiotics results in rapid modification of myeloid cell gene expression and epigenetic state, towards that of healthy volunteers, suggesting that repeated acute inflammatory episodes play an important role in CF inflammatory lung damage.
wMelreplacement of dengue-competent mosquitoes is robust to near-term climate change
Authors: Vásquez Váleri N. , Kueppers Lara M. , Rašić Gordana , Marshall John M.
Published: October 2022

Rising temperatures and increasing temperature variability are impacting the range and prevalence of mosquito-borne disease. A promising biocontrol technology replaces wild mosquitoes with those carrying the virus-blockingWolbachiabacterium. Laboratory and field observations show that the most widely used strain,wMel, is adversely affected by heat stress. Here, we examine whether and how climate warming may impactwMel-based replacement. We integrate empirical data on the temperature sensitivity ofwMelbacteria into a mechanistic model of population dynamics for the dengue vectorAedes aegyptiand use CMIP5 climate projections and historical temperature records from Cairns, Australia to simulate vector control interventions. We show that higher mean temperatures are predicted to lowerwMelinfection frequency and that extended heatwaves have the potential to reverse the public health benefits of this intervention. Sensitivity analysis probing the thermal limits ofwMelreplacement reveal that, under existing projections, operational adaptations would be required for heatwaves lasting longer than two weeks. We conclude that this technology is expected to be robust to both the increased mean temperatures and heatwaves associated with near-term climate change in temperate regions. However, more rapid warming or tropical and inland regions that presently feature hotter baselines may challenge these tested limits, requiring further research.
A penultimate classification of canonical antibody CDR conformations
Authors: Kelow Simon , Faezov Bulat , Xu Qifang , Parker Mitchell , Adolf-Bryfogle Jared , Dunbrack Roland L.
Published: October 2022

Antibody complementarity determining regions (CDRs) are loops within antibodies responsible for engaging antigens during the immune response and in antibody therapeutics and laboratory reagents. Since the 1980s, the conformations of the hypervariable CDRs have been structurally classified into a number of “canonical conformations” by Chothia, Lesk, Thornton, and others. In 2011 (North et al, J Mol Biol. 2011), we produced a quantitative clustering of approximately 300 structures of each CDR based on their length, a dihedral angle metric, and an affinity propagation algorithm. The data have been made available on our PyIgClassify website since 2015 and have been widely used in assigning conformational labels to antibodies in new structures and in molecular dynamics simulations. In the years since, it is has become apparent that many of the clusters are not “canonical” since they have not grown in size and still contain few sequences. Some clusters represent multiple conformations, given the assignment method we have used since 2015. Electron density calculations indicate that some clusters are due to misfitting of coordinates to electron density. In this work, we have performed a new statistical clustering of antibody CDR conformations. We used Electron Density in Atoms (EDIA, Meyder et al., 2017) to produce data sets with different levels of electron density validation. Clusters were chosen by their presence in high electron density cutoff data sets and with sufficient sequences (≥10) across the entire PDB (no EDIA cutoff). About half of the North et al. clusters have been “retired” and 13 new clusters have been identified. We also include clustering of the H4 and L4 CDRs, otherwise known as the “DE loop” which connects strands D and E of the variable domain. The DE loop sometimes contacts antigens and affects the structure of neighboring CDR1 and CDR2 loops. The current database contains 6,486 PDB antibody entries. The new clustering will be useful in the analysis and development of new antibody structure prediction and design algorithms based on rapidly emerging techniques in deep learning. The new clustering data are available athttp://dunbrack2.fccc.edu/PyIgClassify2.
Astrocyte 3D Culture and Bioprinting using Peptide Functionalized Hyaluronan Hydrogels
Authors: Matthiesen Isabelle , Jury Michael , Boroojeni Fatemeh Rasti , Ludwig Saskia L. , Holzreuter Muriel , Buchmann Sebastian , Träger Andrea , Selegård Robert , Winkler Thomas E. , Aili Daniel , Herland Anna
Published: October 2022

The often-forgotten astrocytes play an important role in the central nervous system, contributing to the development of and maintenance of synapses, recycling of neurotransmitters, and the pathophysiology of various neurodegenerative diseases. Hydrogels can provide improved support and attachment for the culture of astrocytes in 3D models, which could further be used to advance clinical in vivo like tissue models of numerous diseases. For full applicability, these gels must be of scalable and defined origin and with stable attachment elements, such as peptides. In this study, the generation of a functional 3D astrocyte model is presented using a hyaluronan-based hydrogel system conjugated with the peptide sequences cyclic RGD (cRGD) and IKVAV, known promoters of cell attachment. Encapsulation of the neuroblastoma cell line SH-SY5Y and glioblastoma cell line U87 is successfully demonstrated over a 6-day culture period. The presence of the peptides cRGD and IKVAV does not change the cells’ viability. Human fetal primary astrocytes (FPA) are further tested for the 3D culture in these materials, similarly, showing that the peptides have no effect on the viability over a 6-day culture period. mRNA expression analysis reveals no biologically significant changes in the 3D cultures FPA or the U87 cells. Morphological analysis, on the other hand, revealed that FPA have a higher degree of interactions with the hyaluronan-based gels compared to the cell lines. This interaction is enhanced by peptide conjugation, in particular cRGD. Finally, we demonstrated that the peptide conjugated hydrogels could be used for bioprinting of FPA, opening up for defined neural astrocytic co-culture.
Aromatic amino acid biosynthesis by aLotusAldolase impacts root hair development and symbiotic associations
Authors: Montiel Jesús , James Euan K. , García-Soto Ivette , Reid Dugald , Napsucialy-Mendivil Selene , Dubrovsky Joseph G. , Cárdenas Luis , Stougaard Jens
Published: October 2022

Legume roots can be symbiotically colonized by arbuscular mycorrhizal (AM) fungi and nitrogen-fixing bacteria. InLotus japonicus, the latter occurs intracellularly by the cognate rhizobial partnerMesorhizobium lotior intercellularly with theAgrobacterium pusenseIRBG74 strain. Although these symbiotic programs show distinctive cellular and transcriptome signatures, some molecular components are shared.

In this study, we demonstrate thatAldolase1, the first enzyme in the biosynthetic pathway of aromatic amino acids (AAA), plays a critical role in root hair development and for AM and rhizobial symbioses inLotus.

Two homozygous mutants affected inAldolase1(ald1-1 andald1-2) show drastic alterations in the root hair morphology, associated with a progressive disruption of the actin cytoskeleton. The altered root hair structure was prevented by chemical and genetic complementation.

Bothald1-1 andald1-2 show significant reductions in rhizobial infection (intracellular and intercellular), nodule organogenesis and AM colonization. RNAseq analysis ofald1-2 roots suggested that these phenotypes are associated with downregulation of several cell wall related genes, and with an attenuated symbiotic signalling. This work provides robust evidence that links AAA metabolism to root hair development and successful symbiotic associations.
Root-knot nematodes produce functional mimics of tyrosine-sulfated plant peptides
Authors: Yimer Henok Zemene , Luu Dee Dee , Blundell Alison Coomer , Ercoli Maria Florencia , Vieira Paulo , Williamson Valerie M. , Ronald Pamela C. , Siddique Shahid
Published: October 2022

Root-knot nematodes (Meloidogynespp.) are highly evolved obligate parasites that threaten global food security. These parasites have a remarkable ability to establish elaborate feeding sites in roots, which are their only source of nutrients throughout their life cycle. A wide range of nematode effectors have been implicated in modulation of host pathways for feeding site development. Plants produce a diverse array of peptide hormones including plant peptides containing sulfated tyrosine (PSYs), which promote root growth via cell expansion and proliferation. A sulfated PSY-like peptide RaxX (required for activation of XA21 mediated immunity X) produced by the biotrophic bacterial pathogen (Xanthomonas oryzaepv.oryzae), has been previously shown to contribute to bacterial virulence. Here, we report the identification of genes from root-knot nematodes predicted to encode PSY-like peptides (MigPSYs) with high sequence similarity to both bacterial RaxX and plant PSYs. Sulfated synthetic peptides corresponding to predicted MigPSYs stimulate root growth in Arabidopsis.MigPSYtranscript levels are highest early in the infection cycle. Down-regulation ofMigPSYgene expression reduces root galling and egg production, suggesting that the MigPSYs serve as nematode virulence factors. Together these results indicate that nematodes and bacteria utilize similar sulfated peptides to hijack plant developmental signaling pathways to facilitate parasitism.
Self-Assembly Coupled to Liquid-Liquid Phase Separation
Authors: Hagan Michael F. , Mohajerani Farzaneh
Published: October 2022

Liquid condensate droplets with distinct compositions of proteins and nucleic acids are widespread in biological cells. While it is known that such droplets can regulate irreversible protein aggregation, their effect on reversible self-assembly remains largely unexplored. In this article, we use kinetic theory and solution thermodynamics to investigate the effect of liquid-liquid phase separation on the reversible self-assembly of structures with well-defined sizes and architectures. We find that when assembling subunits preferentially partition into liquid domains, robustness against kinetic traps and maximum achievable assembly rates can be significantly increased. In particular, the range of solution conditions over which productive assembly and the corresponding assembly rates can increase by orders of magnitude. We analyze the rate equation predictions using simple scaling estimates to identify effect of liquid-liquid phase separation as a function of relevant control parameters. These results may elucidate self-assembly processes that underlie normal cellular functions or pathogenesis, and suggest strategies for designing efficient bottom-up assembly for nanomaterials applications.
Combination of the parent analogue of Remdesivir (GS-441524) and Molnupiravir results in a markedly potent antiviral effect in SARS-CoV-2 infected Syrian hamsters
Authors: Abdelnabi Rana , Maes Piet , de Jonghe Steven , Weynand Birgit , Neyts Johan
Published: October 2022

Remdesivir was the first drug to be approved for the treatment of severe COVID-19; followed by molnupiravir (another prodrug of a nucleoside analogue) and the protease inhibitor nirmatrelvir. Combination of antiviral drugs may result in improved potency and help to avoid or delay the development of resistant variants. We set out to explore the combined antiviral potency of GS-441524 (the parent nucleoside of remdesivir) and molnupiravir against SARS-CoV-2. In SARS-CoV-2 (BA.5) infected A549-Dual™ hACE2-TMPRSS2 cells, the combination resulted in an overall additive antiviral effect with a synergism at certain concentrations. Next, the combined effect was explored in Syrian hamsters infected with SARS-CoV-2 (Beta, B.1.351); treatment was started at the time of infection and continued twice daily for four consecutive days. At 4 day 4 post-infection, GS-441524 (50 mg/kg, oral BID) and molnupiravir (150 mg/kg, oral BID) as monotherapy reduced infectious viral loads by 0.5 and 1.6 log10, respectively, compared to the vehicle control. When GS-441524 (50 mg/kg, BID) and molnupiravir (150 mg/kg, BID) were combined, infectious virus was no longer detectable in the lungs of 7 out of 10 of the treated hamsters (4.0 log10reduction) and titers in the other animals were reduced by ~2 log10. The combined antiviral activity of molnupiravir which acts by inducing lethal mutagenesis and GS-441524, which acts as a chain termination appears to be highly effective in reducing SARS-CoV-2 replication/infectivity. The unexpected potent antiviral effect of the combination warrants further exploration as a potential treatment for COVID-19.
Evidence for a compact σ70conformationin vitroandin vivo
Authors: Joron Khalil , Zamel Joanna , Kalisman Nir , Lerner Eitan
Published: October 2022

The initiation of transcription in Escherichia coli (E. coli) is facilitated by promoter specificity factors, also known as σ factors, which may bind a promoter only as part of a complex with RNA polymerase (RNAP). By performingin vitrocross-linking mass spectrometry (CL-MS) of apo-σ70, we reveal structural features suggesting a compact conformation compared to the known RNAP-bound extended conformation. Then, we validate the existence of the compact conformation usingin vivoCL-MS by identifying cross-links similar to those foundin vitro, which deviate from the extended conformation only during the stationary phase of bacterial growth. Conclusively, we provide information in support of a compact conformation of apo-σ70that exists in live cells, which might represent a transcriptionally-inactive form that can be activated upon binding to RNAP.