bluuebunny/crossref_metadata_2025 huggingface dataset:
Nerve Injury Triggers Time-dependent Activation of the Locus Coeruleus, Influencing Spontaneous Pain-like Behavior in Rats
Authors: Suárez-Pereira Irene , López-Martín Carolina , Camarena-Delgado Carmen , Llorca-Torralba Meritxell , González-Saiz Francisco , Ruiz Rocío , Santiago Martiniano , Berrocoso Esther
Published: April 2024

Background

Dynamic changes in neuronal activity and in noradrenergic locus coeruleus (LC) projections have been proposed during the transition from acute to chronic pain. Thus, the authors explored the cellular cFos activity of the LC and its projections in conjunction with spontaneous pain-like behavior in neuropathic rats.

Methods

Tyrosine hydroxylase:Cre and wild-type Long–Evans rats, males and females, were subjected to chronic constriction injury (CCI) for 2 (short-term, CCI-ST) or 30 days (long-term, CCI-LT), evaluating cFos and Fluoro-Gold expression in the LC, and its projections to the spinal cord (SC) and rostral anterior cingulate cortex (rACC). These tests were carried out under basal conditions (unstimulated) and after noxious mechanical stimulation. LC activity was evaluated through chemogenetic and pharmacologic approaches, as were its projections, in association with spontaneous pain-like behaviors.

Results

CCI-ST enhanced basal cFos expression in the LC and in its projection to the SC, which increased further after noxious stimulation. Similar basal activation was found in the neurons projecting to the rACC, although this was not modified by stimulation. Strong basal cFos expression was found in CCI-LT, specifically in the projection to the rACC, which was again not modified by stimulation. No cFos expression was found in the CCI-LT LCipsilateral (ipsi)/contralateral (contra)→SC. Chemogenetics showed that CCI-ST is associated with greater spontaneous pain-like behavior when the LCipsi is blocked, or by selectively blocking the LCipsi→SC projection. Activation of the LCipsi or LCipsi/contra→SC dampened pain-like behavior. Moreover, Designer Receptor Exclusively Activated by Designer Drugs (DREADDs)–mediated inactivation of the CCI-ST LCipsi→rACC or CCI-LT LCipsi/contra→rACC pathway, or intra-rACC antagonism of α-adrenoreceptors, also dampens pain-like behavior.

Conclusions

In the short term, activation of the LC after CCI attenuates spontaneous pain-like behaviors via projections to the SC while increasing nociception via projections to the rACC. In the long term, only the projections from the LC to the rACC contribute to modulate pain-like behaviors in this model.

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Cost-Effectiveness of Sleeve Gastrectomy and Gastric Bypass as Revisional Surgery on Antidiabetic Reimbursement: A Nationwide Cohort Study
Authors: Thereaux Jérémie , Bennani Mohammed , Khemis Jean , Ohayon Elisabeth , Visnovec Buissez Isabelle , Lafourcade Alexandre , Quiriconi Laëtitia , Philippe Caroline , Oppert Jean-Michel
Published: April 2024

Objective:

This study compared the effectiveness of 4 main revisional bariatric surgery (RBS) sequences after sleeve gastrectomy (SG) and adjustable gastric banding (AGB), on the reimbursement of antidiabetic treatments in France.

Background:

Few large-scale prospective cohort studies have assessed the changes in antidiabetic treatments after RBS.

Method:

This nationwide observational population-based cohort study analyzed data from the French National Health Insurance Database. All patients who underwent primary SG and AGB in France between January 2012 and December 2014 were included and followed up until December 31, 2020. The changes in categories and costs of reimbursed antidiabetic treatments across different RBS sequences were assessed (presented as follows: bariatric surgery (BS)-RBS).

Results:

Among the 107,088 patients who underwent BS, 6396 underwent RBS, 2400 SG-GBP (SG converted to gastric bypass [GBP] during follow-up), 2277 AGB-SG, 1173 AGB-GBP, and 546 SG-SG. Pre-RBS insulin was used in 10 (2.9%), 4 (0.9%), 8 (2.4%), and 10 (2.6%) patients, respectively. Two years after RBS, the treatment discontinuation or decrease (the change of treatment to a lighter one category rates [eg, insulin to bi/tritherapy]) was 47%, 47%, 49%, and 34%, respectively. Four years after RBS, the median annual cost per patient compared with baseline was lower (P < 0.01) for all sequences, except SG-SG (P = 0.24). The most notable effect concerned AGB-GBP (median of more than 220 euros to 0).

Conclusions:

This study demonstrated the positive impact of RBS over a 4-year follow-up period on antidiabetic treatments reimbursement, through the reduction or discontinuation of treatments and a significant decrease in costs per patient.
Use of Darvadstrocel (Allogenic Stem Cell Therapy) for Crohn’s Fistulas in Real Clinical Practice: The National Project to Implement Mesenchymal Stem Cell for the Treatment of Perianal Crohn’s Fistula (the PRIME Study)
Authors: Herreros Maria Dolores , Ramirez Jose-Manuel , Otero-Piñeiro Ana M. , Martí-Gallostra Marc , Badiola Izaskun , Enríquez-Navascues Jose M. , Millan Monica , Barreiro Erica , de la Portilla de Juan Fernando , Suárez Alecha Javier , Garcia-Olmo Damian ,   The National Project to Implement Mesenchymal Stem Cell for the Treatment of Perianal Crohn’s Fistula (the PRIME Study) Group
Published: April 2024

BACKGROUND:

Perianal fistulas may affect 15–50% of patients with Crohn’s disease. Treatment is complex, requiring a multidisciplinary approach. Darvadstrocel (allogenic mesenchymal cells obtained from lipoaspirates) was approved in 2018 by the European and Spanish Agencies of Medicines and Medical Products as a treatment for fistulas in Crohn’s disease. Recent European Crohn’s and Colitis Organisation and Spanish Working Group on Crohn’s Disease and Ulcerative Colitis guidelines state that darvadstrocel is effective with a favorable safety profile and a strong level of evidence (2).

OBJECTIVE:

Presenting real-world effectiveness data for darvadstrocel in a Spanish population.

DESIGN:

Observational retrospective cohort study with prospective data gathering.

SETTINGS:

Fourteen institutions.

PATIENTS:

From November 2019-April 2022, all patients (73) treated with darvadstrocel in these institutions were included, fulfilling the following criteria: 1) complex fistula/s in a patient with Crohn’s disease; 2) failure of conventional and antitumor necrosis factor treatment; 3) absence of collections >2 cm confirmed by pelvic MRI scan at the time of surgery.

INTERVENTIONS:

Darvadstrocel treatment.

MAIN OUTCOME MEASURES:

Clinical response (closure of ≥50% of external openings), complete clinical closure (100% of external openings) and radiological closure (no fluid collection >2 cm, no edema or inflammation) evaluated 6 months after treatment.

RESULTS:

Clinical response was observed in 63 patients (86.3%), complete clinical closure in 50 patients (68.5%) and radiological closure in 45 patients (69.2%). Combined clinical and radiological response was observed in 41 patients (63.1%). Not all clinically healed patients had radiological closure and vice versa. No serious adverse events were reported.

LIMITATIONS:

Retrospective.

CONCLUSIONS:

Study results were consistent with those reported in previous clinical trials, real-world efficacy findings from the INSPIRE study (assessing darvadstrocel effectiveness in Europe, Israel, Switzerland, UK, and Japan) and previously published literature. Darvadstrocel was effective and demonstrated a favorable safety profile when used in normal clinical practice for treatment of fistulas in Crohn’s disease. See Video Abstract.
Prevention and treatment of hypertensive left ventricular hypertrophy
Authors: Tatavarthy Manvita , Stathopoulos John , Oktay Ahmet Afşin
Published: April 2024

Purpose of review

Left ventricular (LV) hypertrophy (LVH) is a well recognized target organ adaptation to longstanding uncontrolled hypertension and other cardiovascular risk factors. It is also a strong and independent predictor of many cardiovascular disorders.

Recent findings

This focused review explores the current concepts in screening, diagnosis, prevention, and treatment of LVH in patients with hypertension. Currently, the primary screening and diagnostic tools for LVH are ECG and 2D echocardiography. Implementing machine learning in the diagnostic modalities can improve sensitivity in the detection of LVH. Lifestyle modifications, blood pressure control with antihypertensive therapy, and management of comorbidities aid in preventing and reversing LV remodeling.

LVH is a common and often silent complication of hypertension. Prevention and reversal of LV remodeling are crucial for cardiovascular risk reduction in patients with hypertension.
Current state of endothelial cell therapy
Authors: Koo Ellen H.
Published: April 2024

Purpose of review

Currently, there is heightened interest surrounding endothelial cell therapy for the treatment of corneal edema. The purpose of this review article is to describe and summarize the background information as well as the research surrounding the emerging treatment modalities for endothelial cell therapy.

Recent findings

Marked advancements have been made in the translational research in this area, and increasing refinements have been demonstrated in the treatment protocols for cell therapy. Human clinical trials in this field are ongoing, specifically, in the area of injected human corneal endothelial cells (HCECs), with early results showing favorable safety and efficacy profiles.

Efficient and effective delivery of HCECs to patients with corneal edema and dysfunction now appears feasible, and the results from ongoing human clinical trials are much anticipated. Adjunct therapeutics—in the form of pharmacological agents and/or surgical techniques, such as descemetorhexis—will likely continue to play an important role in defining the future of endothelial cell therapy.
Legislative Health Notes: Preliminary Learnings From Piloting a New Policy Analysis Tool
Authors: Carignan Stefanie , Lindberg Ruth , Tung Gregory J. , Sullivan Jennifer , Stone Cynthia , Pollack Porter Keshia M.
Published: April 2024

Context:

In 2018, the Health Impact Project (the Project) developed and tested a new health in all policies (HiAP) tool called “legislative health notes” to provide state and local legislators with peer-reviewed evidence, public health data, and local data that illustrate potential positive and negative health and equity effects of proposed bills.

Objectives:

The Project sought to refine the health note methodology while piloting the tool in the Colorado and Indiana General Assemblies, and with the Council of the District of Columbia, and worked with affiliates to introduce them in North Carolina, Ohio, and California.

Design and Participants:

External partners solicited feedback on health notes via semistructured interviews and surveys from legislators, legislative staff, and expert reviewers who were familiar with health notes in each of these jurisdictions.

Results:

Respondents shared that health notes were nonpartisan, were easy for nonexperts to understand, and would be more effective if delivered earlier in the legislative process.

Conclusion:

In response to informant feedback, practitioners can explore adding high-level summaries, increasing focus on health equity implications and the potential to work with legislators during the policy formulation phase. Data from this pilot suggest that legislative health notes are a promising nonpartisan and standardized tool to better understand the health and equity implications of proposed legislation.
From Research to Roach Traps: Practical Considerations for a Home-Based Asthma Program
Authors: Talis Natalie , Lewis Nathaniel , Doraiswamy Prakash , Wu Zhiyong , Boakye Brittney
Published: April 2024

Context:

Home-based asthma interventions have a significant evidence base as an effective means to address moderate and severe breathing concerns triggered by home conditions. However, the literature lacks logistical and staffing considerations necessary to successfully implement such a program at a governmental level. This practice report and process evaluation outlines practical details and lessons learned during a healthy homes pilot, and how they were addressed in the design of a permanent program.

Objective:

To inform the creation of a permanent home-based asthma intervention at the Alexandria Health Department (AHD) (City of Alexandria, Virginia) and understand the tools and resources necessary for success.

Intervention:

Participating households received a health and environmental assessment, followed by cleaning supplies, relevant education, and referrals to partners for services. AHD staff tracked challenges and insights at each step of the intervention. At the end of the pilot, staff worked with the community to identify solutions and design a permanent program.

Conclusions:

Although the pilot model was constructed based on existing case studies, technical assistance from national experts, and guidance documents, the team still experienced challenges around recruitment, staff support, home visit implementation, and impact evaluation. While pilots and existing literature can be instructive for identifying issues, work with residents and partners to develop a uniquely tailored community program was essential for practical success.

Implications on Policy and Practice:

Health departments developing new initiatives should consider both the staff and participant experience throughout the creation of administrative and programmatic processes. Testing out draft versions of these processes and materials using internal and external focus groups can identify potential bottlenecks and solutions upfront.
Reaching Diverse Communities During a Local Public Health COVID-19 Vaccination Response Through a Mobile Clinic Compared to Mass Vaccination Sites
Authors: Gavin Regina M. , Countryman Melanie , Musco Joseph , Ricard Rachel , Roberts Amalia , Lees Christine
Published: April 2024

During the COVID-19 vaccine rollout, local public health agencies were responsible for vaccinating a wide variety of communities. Dakota County Public Health (Dakota County, Minnesota) implemented a program that offered COVID-19 vaccines in a variety of settings, such as county public health buildings, community sites, in-home, mass vaccination clinics, and a mobile clinic unit. The purpose of this analysis is to compare the demographics of vaccinations administered at Dakota County COVID-19 vaccination clinics based on clinic site. More than half (52.5%) of vaccinations administered at mobile clinic sites were administered to Hispanic or Latino clients, while at the mass vaccination clinic site, 5.4% of vaccinations were administered to Hispanic or Latino clients. In addition, 59.6% of in-home vaccinations were administered to adults 65 years and older. Offering COVID-19 vaccination clinics in a variety of clinic settings strategically throughout the community helped increase vaccine reach to diverse communities.
Home Visiting in California During the First Two Years of the COVID-19 Pandemic: A Repeated Cross-Sectional Study of Low-Income Pregnant and Parenting Caregivers
Authors: Franck Linda S. , Mehra Renee , Remy Linda , Rienks Jennifer
Published: April 2024

Context:

Prior to the COVID-19 pandemic, home visiting services for low-income children and families were provided almost entirely in person. Little is known about clients’ experience of home visiting provided virtually by video or phone instead of, or in addition to, in-person home visiting.

Objective:

To explore the views of clients in the California Work Opportunity and Responsibility to Kids (CalWORKs) Home Visiting Program (HVP) across California during the first 2 years of the pandemic.

Setting:

Forty counties in California.

Participants:

CalWORKs HVP clients, currently enrolled or who left the program in the 6 months prior to each survey.

Main Outcome Measures:

Clients’ ratings of participation in and experiences with the CalWORKs HVP services, as well as unmet needs.

Results:

We collected 1617 surveys from clients across 3 survey rounds. Pandemic-related restrictions resulted in decreased frequency of home visits and a shift from in person to primarily virtual visits. As in-person home visit frequency decreased, there were significant declines in clients’ level of agreement that they learned child development skills (P = .04), received parenting services (P = .015) or activities (P < .001), or received infant and child nutrition services (P = .003). There were no declines in level of agreement that the CalWORKs HVP improved the quality of life of clients and their children.

Discussion:

Clients consistently rated the CalWORKs HVP as positively contributing to their and their children’s well-being, regardless of the shift from in person to virtual visits. Clients’ participation in some program components decreased over the evaluation. However, it is unknown if clients received fewer referrals, were hesitant to pursue the referrals, or if fewer services were available. Continued research is needed to evaluate the merits and disadvantages of virtual visits as in-person home visits resume postpandemic.
Complexity biomechanics: a case study of dragonfly wing design from constituting composite material to higher structural levels
Authors: Toofani Arman , Eraghi Sepehr H. , Basti Ali , Rajabi Hamed
Published: April 2024

Presenting a novel framework for sustainable and regenerative design and development is a fundamental future need. Here we argue that a new framework, referred to as complexity biomechanics, which can be used for holistic analysis and understanding of natural mechanical systems, is key to fulfilling this need. We also present a roadmap for the design and development of intelligent and complex engineering materials, mechanisms, structures, systems, and processes capable of automatic adaptation and self-organization in response to ever-changing environments. We apply complexity biomechanics to elucidate how the different structural components of a complex biological system as dragonfly wings, from ultrastructure of the cuticle, the constituting bio-composite material of the wing, to higher structural levels, collaboratively contribute to the functionality of the entire wing system. This framework not only proposes a paradigm shift in understanding and drawing inspiration from natural systems but also holds potential applications in various domains, including materials science and engineering, biomechanics, biomimetics, bionics, and engineering biology.
Structural diversity of crustacean exoskeletons and its implications for biomimetics
Authors: Vittori Miloš
Published: April 2024

The crustacean cuticle is a biological composite material consisting of chitin–protein fibres in a mineralized matrix. Recent research has revealed a surprising range of fibre architectures and mineral compositions of crustacean skeletal structures adapted to various mechanical demands. It is becoming increasingly clear that the organic fibres in the cuticle may be organized in patterns differing from the standard twisted plywood model. Observed fibre architectures in protruding skeletal structures include longitudinal and circular parallel fibre arrays. Skeletal minerals often include calcium phosphates in addition to calcium carbonates. Furthermore, skeletal properties are affected by protein cross-linking, which replaces mineralization as a stiffening mechanism in some structures. Several common structural motifs, such as the stiffening of the outer skeletal layers, the incorporation of non-mineralized cuticle in exposed structures, and interchanging layers of parallel fibres and the twisted plywood structure, can be identified in skeletal elements with similar functions. These evolutionary solutions have the potential for biomimetic applications, particularly as manufacturing technologies advance. To make use of this potential, we need to understand the processes behind the formation of the crustacean exoskeleton and determine which features are truly adaptive and worth mimicking.
Micromonospora cathayae sp. nov., isolated from the rhizosphere soil of Cathaya argyrophylla
Authors: Long Pei-Lan , Fu Li , Xiao Yan , Gao Jian
Published: April 2024

A novel actinobacterium, strain HUAS 3T, was isolated from the rhizosphere soil of Cathaya argyrophylla collected in Hunan Province, PR China. Strain HUAS 3T contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The dominant menaquinones were MK-9(H4), MK-9(H6), MK-10(H2) and MK-9(H4). The polar lipids consisted of diphosphatidylglycerol, phospholipids, phosphatidylethanolamine, phosphatidylglycerol, phosphotidylinositol and phosphatidylinositol mannosides. The main cellular fatty acids (>5.0 %) were C17 : 1 ω8c, iso-C16 : 0, C18 : 1 ω9c, iso-C15 : 0, C16 : 0 and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c). The DNA G+C content of the novel strain's genome sequence, consisting of 7 196 442 bp, was 72.8 mol%. The full-length 16S rRNA gene sequence analysis indicated that strain HUAS 3T belonged to the genus Micromonospora and showed highest similarities to Micromonospora fluminis A38T (99.44 %), Micromonospora echinospora DSM 43816T (99.23 %), Micromonospora tulbaghiae DSM 45142T (99.23 %), Micromonospora solifontis PPF5-17T (99.16 %) and Micromonospora endolithica DSM 44398T (98.96 %). Phylogenetic trees based on 16S rRNA gene sequences showed that strain HUAS 3T was closely related to M. fluminis A38T, M. tulbaghiae DSM 45142T and M. solifontis PPF5-17T. The phylogenomic tree revealed that strain HUAS 3T was closely related to Micromonospora pallida DSM 43817T. However, the average nucleotide identity (ANIb/ANIm) and the digital DNA–DNA hybridization values between them were 84.75 /88.16 and 30.80 %, respectively, far less than the 95–96 and 70 % cut-off points recommended for delineating species. Furthermore, strain HUAS 3T was distinct from the type strain of M. pallida in terms of phenotypic and chemotaxonomic characteristics. In summary, strain HUAS 3T represents a novel Micromonospora species, for which the name Micromonospora cathayae sp. nov. is proposed. The type strain is HUAS 3T (=MCCC 1K08599T=JCM 36275T).
Kaistella rhinocerotis sp. nov., isolated from the faeces of rhinoceros and reclassification of Chryseobacterium faecale as Kaistella faecalis comb. nov.
Authors: Park Yerim , Min Jihyeon , Kim Wonjae , Park Woojun
Published: April 2024

Strain Ran72T, a novel Gram-stain-negative, obligately aerobic, non-motile, and rod-shaped bacterium, was isolated from the faeces of the rhinoceros species Ceratotherium simum. The novel bacterial strain grew optimally in Reasoner's 2A medium under the following conditions: 0 % (w/v) NaCl, pH 7.5, and 30 °C. Based on phylogenetic analysis using 16S rRNA gene sequencing, strain Ran72T was found to be most closely related to Chryseobacterium faecale F4T (98.4 %), Kaistella soli DKR-2T (98.0 %), and Kaistella haifensis H38T (97.4 %). A comprehensive genome-level comparison between strain Ran72T with C. faecale F4T, K. soli DKR-2T, and K. haifensis H38T revealed average nucleotide identity, digital DNA–DNA hybridization, and average amino acid identity values of ≤74.9, ≤19.3, and ≤78.7 %, respectively. The major fatty acids were anteiso-C15 : 0 (22.3 %), with MK-6 being the predominant respiratory quinone. The major polar lipids of strain Ran72T were phosphatidylethanolamine, four unidentified aminolipids, and two unidentified lipids. Based on our chemotaxonomic, genotypic, and phenotype characterizations, strain Ran72T was identified as representing a novel species in the genus Kaistella, for which the name Kaistella rhinocerotis sp. nov. is proposed, with the type strain Ran72T (=KACC 23136T=JCM 36038T). Based on the outcomes of our phylogenomic study, Chryseobacterium faecale should be reclassified under the genus Kaistella as Kaistella faecalis comb. nov.
Molecular and biological characterization of a bunyavirus infecting the brown planthopper (Nilaparvata lugens)
Authors: Li Ting , Ye Zhuang-Xin , Feng Ke-Hui , Mao Qian-Zhuo , Hu Qing-Ling , Zhuo Ji-Chong , Zhang Chuan-Xi , Chen Jian-Ping , Li Jun-Min
Published: April 2024

A negative-strand symbiotic RNA virus, tentatively named Nilaparvata lugens Bunyavirus (NLBV), was identified in the brown planthopper (BPH, Nilaparvata lugens). Phylogenetic analysis indicated that NLBV is a member of the genus Mobuvirus (family Phenuiviridae, order Bunyavirales). Analysis of virus-derived small interfering RNA suggested that antiviral immunity of BPH was successfully activated by NLBV infection. Tissue-specific investigation showed that NLBV was mainly accumulated in the fat-body of BPH adults. Moreover, NLBV was detected in eggs of viruliferous female BPHs, suggesting the possibility of vertical transmission of NLBV in BPH. Additionally, no significant differences were observed for the biological properties between NLBV-infected and NLBV-free BPHs. Finally, analysis of geographic distribution indicated that NLBV may be prevalent in Southeast Asia. This study provided a comprehensive characterization on the molecular and biological properties of a symbiotic virus in BPH, which will contribute to our understanding of the increasingly discovered RNA viruses in insects.
A historical sequence deletion in a commonly used Bacillus subtilis chromosome integration vector generates undetected loss-of-function mutations
Authors: Dierksheide K. Julia , Li Gene-Wei
Published: April 2024

Since the 1980s, chromosome-integration vectors have been used as a core method of engineering Bacillus subtilis. One of the most frequently used vector backbones contains chromosomally derived regions that direct homologous recombination into the amyE locus. Here, we report a gap in the homology region inherited from the original amyE integration vector, leading to erroneous recombination in a subset of transformants and a loss-of-function mutation in the downstream gene. Internal to the homology arm that spans the 3′ portion of amyE and the downstream gene ldh, an unintentional 227 bp deletion generates two crossover events. The major event yields the intended genotype, but the minor event, occurring in ~10 % of colonies, results in a truncation of ldh, which encodes lactate dehydrogenase. Although both types of colonies test positive for amyE disruption by starch plating, the potential defect in fermentative metabolism may be left undetected and confound the results of subsequent experiments.
Transcriptome Analysis Reveals Long-Term Somatic Memory of Stress in The Woody Perennial Crop, GrapevineVitis Viniferacv. Cabernet Sauvignon
Authors: Tan Jia W. , Tesfamicael Kiflu , Hu Yikang , Shinde Harshraj , Edwards Everard J. , Tricker Penny , Lopez Carlos Marcelino Rodriguez
Published: April 2024

Plants can generate a molecular memory of stress resulting in primed plants that are more resilient to subsequent stresses occurring days to weeks after the priming event. Whether such a priming effect is maintained over longer periods, and after winter dormancy in perennial plants, is less studied. Here, we used whole transcriptome and methylome sequencing of grapevine plants over two growing seasons to characterize grapevines’ response to combined drought and heat stress in naïve and primed plants. Our results showed changes in expression of genes associated with epigenetic modifications during stress and after stress removal, suggesting the establishment of epigenetic memory of stress. Primed plants had a small number of differentially expressed genes associated with stress response one year after the priming event even in the absence of second stress and presented a stronger transcriptional response than naïve plants when re-exposed to stress. Methylome analysis revealed an increase in DNA methylation in primed vines under combined stress, and that methylation patterns were less variable among plants under stress than control plants. We did not observe any correlation between DNA methylation and gene transcription, suggesting that stress-induced expression changes were, at least partially, independent of DNA methylation, with posttranscriptional regulation and histone modifications more likely candidates in the establishment of epigenetic memory. Additionally, we characterized stress responsive genes based on their transcriptional profile and function and propose a new comprehensive and intuitive classification model for stress memory genes in perennials.
Lgr5+ intestinal stem cells are required for organoid survival after genotoxic injury
Authors: Lee Joseph , Gleizes Antoine , Takaesu Felipe , Webster Sarah F , Hailstock Taylor , Barker Nick , Gracz Adam D
Published: April 2024

Progenitors and mature cells can maintain the intestinal epithelium by dedifferentiation and facultative intestinal stem cell (fISC) function when active ISCs (aISCs) are lost to damage. Here, we sought to model fISC activation in intestinal organoids with doxorubicin (DXR), a chemotherapeutic known to ablateLgr5+ aISCsin vivo. We identified low and high doses of DXR compatible with long-term organoid survival. Similar fISC gene activation was observed between organoids treated with low vs high DXR, despite significantly decreased survival at the higher dose. aISCs exhibit dose-dependent loss after DXR but survive at doses compatible with organoid survival. We ablated residual aISCs after DXR using aLgr52A-DTRallele and observed that aISC survival of the initial genotoxic insult is required for organoid survival following DXR. These results suggest that while typical fISC genes are activated by DXR injury in organoids, functional stemness remains dependent on the aISC pool. Our data establish a reproducible model of DXR injury in intestinal organoids and reveal differences inin vitroresponses to an establishedin vivodamage modality.
On use of tertiary structure characters in hidden Markov models for protein fold prediction
Authors: Malik Ashar J. , Puente-Lelievre Caroline , Matzke Nicholas , Ascher David B.
Published: April 2024

While advances in protein structure prediction have opened up insights into arcane proteins, weak sequence homology makes functional characterisation challenging. To overcome this challenge, we use structure-based hidden Markov models of groupings in SCOP, CATH and ECOD to predict folds in proteins and thereby infer function. Conservation of structure and ability of hidden Markov models to detect remote signals make this a powerful resource for complete characterisation of arcane proteins.
Comprehensive evaluation and prediction of editing outcomes for near-PAMless adenine and cytosine base editors
Authors: Zhou Xiaoyu , Gao Jingjing , Luo Liheng , Huang Changcai , Wu Jiayu , Wang Xiaoyue
Published: April 2024

Base editors enable the direct conversion of target bases without inducing double-strand breaks, showing great potential for disease modeling and gene therapy. Yet, their applicability has been constrained by the necessity for specific protospacer adjacent motif (PAM). We generated four versions of near-PAMless base editors and systematically evaluated their editing patterns and efficiencies using an sgRNA-target library of 45,747 sequences. Near-PAMless base editors significantly expanded the targeting scope, with both PAM and target flanking sequences as determinants for editing outcomes. We developed BEguider, a deep learning model to accurately predict editing results for near-PAMless base editors. We also provided experimentally measured editing outcomes of 20,541 ClinVar sites, demonstrating that variants previously inaccessible by NGG PAM base editors can now be precisely generated or corrected. We have made our predictive tool and data available online to facilitate development and application of near-PAMless base editors in both research and clinical settings.
The Class III peroxidase OsPrx20 is a key regulator of stress response and growth in rice
Authors: Shen Tao , Wang Qingwen , Chen Dan , Ju Huining , Yan Runjiao , Xu Fengjuan , Fu Donghuan , Bu Xiaona , Zhang Huan , Hu Jiexiong , Zhang Zhengguang , Ni Lan , Jiang Mingyi
Published: April 2024

In plants, reactive oxygen species maintain strictly low intracellular levels that is prerequisite for their function as second messengers. However, abiotic and biotic stresses are also long-term processes, requiring rapid scavenging of excess intracellular ROS. Plant Class III peroxidases, as multifunctional enzymes, are core enzymes in regulating intracellular ROS homeostasis and are key to regulating the complicated signaling network. Here, we found a rice Class III peroxidase OsPrx20 maintains intracellular ROS homeostasis in different conditions. OsPrx20 is a target of Ca2+/calmodulin-dependent protein kinase (OsDMI3) and phosphorylates its Thr-244 site by OsDMI3. Overexpression ofOsPrx20enhances osmotic stress tolerance but reduces blast resistance, while lack ofOsPrx20is opposite, suggesting OsPrx20 positively regulates osmotic stress tolerance but negatively regulates blast resistance in rice. Meanwhile, overexpression ofOsPrx20enlarges spike size and grain fullness, whereas lack ofOsPrx20leads to dwarfism and smaller spike. In ABA signaling, OsPrx20 Thr-244 phosphorylation is specifically dependent on OsDMI3 to reduce the sensitivity of ABA to seed germination and root growth and to enhance osmotic stress tolerance without affecting spike and grain development. Our study reveals an essential regulatory mechanism that directly activates OsPrx20 in ABA signaling, highlighting the multi-functionality of OsPrx20 in different biological processes.
Emergentemm4group AStreptococcusevidences a survival strategy during interaction with immune effector cells
Authors: Odo Chioma M. , Vega Luis A , Mukherjee Piyali , DebRoy Sruti , Flores Anthony R. , Shelburne Samuel A.
Published: April 2024

The major gram-positive pathogen group AStreptococcus(GAS) is a model organism for studying microbial epidemics as it causes waves of infections. Since 1980, several GAS epidemics have been ascribed to the emergence of clones producing increased amounts of key virulence factors such as streptolysin O (SLO). Herein, we sought to identify mechanisms underlying our recently identified temporal clonal emergence amongstemm4GAS, given that emergent strains did not produce augmented levels of virulence factors relative to historic isolates. Through the creation and analysis of isoallelic strains, we determined that a conserved mutation in a previously undescribed gene encoding a putative carbonic anhydrase was responsible for the defectivein vitrogrowth observed in the emergent strains. We also identified that the emergent strains survived better inside macrophages and killed macrophages at lower rates relative to the historic strains. Via creation of isogenic mutant strains, we linked the emergent strain “survival” phenotype to the downregulation of the SLO encoding gene and upregulation of themsrABoperon which encodes proteins involved in defense against extracellular oxidative stress. Our findings are in accord with recent surveillance studies which found high ratio of mucosal (i.e., pharyngeal) relative to invasive infections amongstemm4GAS. Inasmuch as ever-increasing virulence is unlikely to be evolutionary advantageous for a microbial pathogen, our data furthers understanding of the well described oscillating patterns of virulent GAS infections by demonstrating mechanisms by which emergent strains adapt a “survival” strategy to outcompete previously circulating isolates.
The G1/S transition in mammalian stem cellsin vivois autonomously regulated by cell size
Authors: Xie Shicong , Zhang Shuyuan , de Medeiros Gustavo , Liberali Prisca , Skotheim Jan M.
Published: April 2024

Cell growth and division must be coordinated to maintain a stable cell size, but how this coordination is implemented in multicellular tissues remains unclear. In unicellular eukaryotes, autonomous cell size control mechanisms couple cell growth and division with little extracellular input. However, in multicellular tissues we do not know if autonomous cell size control mechanisms operate the same way or whether cell growth and cell cycle progression are separately controlled by cell-extrinsic signals. Here, we address this question by tracking single epidermal stem cells growing in adult mice. We find that a cell-autonomous size control mechanism, dependent on the RB pathway, sets the timing of S phase entry based on the cell’s current size. Cell-extrinsic variations in the cellular microenvironment affect cell growth rates but not this autonomous coupling. Our work reassesses long-standing models of cell cycle regulation within complex metazoan tissues and identifies cell-autonomous size control as a critical mechanism regulating cell divisionsin vivoand thereby a major contributor to stem cell heterogeneity.
Photochromic reversion enables long-term tracking of single molecules in living plants
Authors: von Arx Michelle , Xhelilaj Kaltra , Schulz Philip , zur Oven-Krockhaus Sven , Gronnier Julien
Published: April 2024

Single-molecule imaging promises the observation of individual molecules at work in living cells1,2. In plants, however, the tracking of single molecules is generally limited to mere hundred milliseconds3–5, making it virtually impossible to observe live dynamic cellular events with molecular resolution. Here, we introduce photochromic reversion which uses the reversion of EOS fluorescent protein’s dark state upon blue light illumination6, thereby stabilizing the fluorescent state of single molecules and extending single-molecule tracking in single particle tracking photoactivated localization microscopy (spt-PALM) experiments. Utilizing photochromic reversion, we tracked single molecules over micrometre distances for seconds. We captured transient spatial arrest events of plasma membrane proteins indicative of the observation of dynamic cellular events under physiological conditions. Finally, we implemented an analysis pipeline leveraging machine learning-based diffusional fingerprinting to automatically detect and quantify spatial arrestment, allowing precise kinetic measurements of molecular events at the nanoscale. We envision that photochromic reversion will constitute a pivotal instrument to decipher fundamental principles underlying membrane dynamics and function in plants.
Coupling of cell growth modulation to asymmetric division and cell cycle regulation inCaulobacter crescentus
Authors: Glenn Skye , Lin Wei-Hsiang , Papagiannakis Alexandros , Kato Setsu , Jacobs-Wagner Christine
Published: April 2024

In proliferating bacteria, growth rate is often assumed to be similar between daughter cells. However, most of our knowledge of cell growth derives from studies on symmetrically dividing bacteria. In many α-proteobacteria, asymmetric division is a normal part of the life cycle, with each division producing daughter cells with different sizes and fates. Here, we demonstrate that the functionally distinct swarmer and stalked daughter cells produced by the model α-proteobacteriumCaulobacter crescentushave different average growth rates despite sharing an identical genome and environment. The discrepancy in growth rate is due to a growth slowdown during the cell cycle stage preceding DNA replication (the G1 phase), which is predominantly associated with swarmer cell functionality. We also provide evidence that the second messenger (p)ppGpp extends the timing of the G1/swarmer cell stage by slowing growth specifically during the beginning of the cell cycle. Our data further show that cells factor the amount and rate of their growth to control the G1/S transition, allowing them to adjust the time they spend with ecologically important G1-specific traits.

Significance statement

Bacterial growth rate modulation is generally associated with changes in genetic make-up or environmental condition. This study demonstrates that the rate of cell growth can also vary between daughter cells and across cell cycle stages under invariant and unstressed environmental conditions. This is illustrated by the asymmetrically dividing α-proteobacteriumCaulobacter crescentus, which, at each division, produces two functionally distinct daughter cells that differ in average growth rate. This growth rate difference arises from a G1 phase-specific growth slowdown mediated, in part, by the (p)ppGpp alarmone. Altogether, this study showcases the coupling of cell growth modulation to asymmetric division and cell cycle regulation, which may have implications for other α-proteobacteria given their cell cycle similarities withC. crescentus.
IAPP Marks Mono-hormonal Stem-cell Derived β Cells that Maintain Stable Insulin Productionin vitroandin vivo
Authors: Davis Jeffrey C. , Ryaboshapkina Maria , Kenty Jennifer H. , Eser Pınar Ö. , Menon Suraj , Tyrberg Björn , Melton Douglas A.
Published: April 2024

Islet transplantation for treatment of diabetes is limited by availability of donor islets and requirements for immunosuppression. Stem cell-derived islets might circumvent these issues. SC-islets effectively control glucose metabolism post transplantation, but do not yet achieve full functionin vitrowith current published differentiation protocols. We aimed to identify markers of mature subpopulations of SC-β cells by studying transcriptional changes associated within vivomaturation of SC-β cells using RNA-seq and co-expression network analysis. The β cell-specific hormone islet amyloid polypeptide (IAPP) emerged as the top candidate to be such a marker. IAPP+cells had more mature β cell gene expression and higher cellular insulin content than IAPP-cellsin vitro. IAPP+INS+cells were more stable in long-term culture than IAPP-INS+cells and retained insulin expression after transplantation into mice. Finally, we conducted a small molecule screen to identify compounds that enhance IAPP expression. Aconitine up-regulated IAPP and could help to optimize differentiation protocols.

Highlights

IAPP expressionin vitromarks a mono-hormonal subpopulation of SC-β cells excluding endocrine hormones other than insulin

Only INS+IAPP+cells maintain stableINSexpressionin vitroup to 100 days after differentiation

The small molecule aconitine accelerates IAPP expression in SC-β cellsin vitro
Glia-derived secretory fatty acid binding protein Obp44a regulates lipid storage and efflux in the developingDrosophilabrain
Authors: Yin Jun , Chen Hsueh-Ling , Grigsby-Brown Anna , He Yi , Cotten Myriam L. , Short Jacob , Dermady Aidan , Lei Jingce , Gibbs Mary , Cheng Ethan S. , Zhang Dean , Long Caixia , Xu Lele , Zhong Tiffany , Abzalimov Rinat , Haider Mariam , Sun Rong , He Ye , Zhou Qiangjun , Tjandra Nico , Yuan Quan
Published: April 2024

Glia derived secretory factors play diverse roles in supporting the development, physiology, and stress responses of the central nervous system (CNS). Through transcriptomics and imaging analyses, we have identified Obp44a as one of the most abundantly produced secretory proteins fromDrosophilaCNS glia. Protein structure homology modeling and Nuclear Magnetic Resonance (NMR) experiments reveal Obp44a as a fatty acid binding protein (FABP) with a high affinity towards long-chain fatty acids in both native and oxidized forms. Further analyses demonstrate that Obp44a effectively infiltrates the neuropil, traffics between neuron and glia, and is secreted into hemolymph, acting as a lipid chaperone and scavenger to regulate lipid and redox homeostasis in the developing brain. In agreement with this essential role, deficiency of Obp44a leads to anatomical and behavioral deficits in adult animals and elevated oxidized lipid levels. Collectively, our findings unveil the crucial involvement of a noncanonical lipid chaperone to shuttle fatty acids within and outside the brain, as needed to maintain a healthy brain lipid environment. These findings could inspire the design of novel approaches to restore lipid homeostasis that is dysregulated in CNS diseases.
Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC
Authors: Smith Byron J. , Zhao Chunyu , Dubinkina Veronika , Jin Xiaofan , Zahavi Liron , Shoer Saar , Moltzau-Anderson Jacqueline , Segal Eran , Pollard Katherine S.
Published: April 2024

Metagenomics has greatly expanded our understanding of the human gut microbiome by revealing a vast diversity of bacterial species within and across individuals. Even within a single species, different strains can have highly divergent gene content, affecting traits such as antibiotic resistance, metabolism, and virulence. Methods that harness metagenomic data to resolve strain-level differences in functional potential are crucial for understanding the causes and consequences of this intraspecific diversity. The enormous size of pangenome references, strain mixing within samples, and inconsistent sequencing depth present challenges for existing tools that analyze samples one at a time. To address this gap, we updated the MIDAS pangenome profiler, now released as version 3, and developed StrainPGC, an approach to strain-specific gene content estimation that combines strain tracking and correlations across multiple samples. We validate our integrated analysis using a complex synthetic community of strains from the human gut and find that StrainPGC outperforms existing approaches. Analyzing a large, publicly available metagenome collection from inflammatory bowel disease patients and healthy controls, we catalog the functional repertoires of thousands of strains across hundreds of species, capturing extensive diversity missing from reference databases. Finally, we apply StrainPGC to metagenomes from a clinical trial of fecal microbiota transplantation for the treatment of ulcerative colitis. We identify twoEscherichia colistrains from two different donors that are both frequently transmitted to patients, but have notable differences in functional potential. StrainPGC and MIDAS v3 together enable precise, intraspecific pangenomic investigations using large collections of metagenomic data without microbial isolation or de novo assembly.
Challenging Backpropagation: Evidence for Target Learning in the Cortex
Authors: Aceituno Pau Vilimelis , de Haan Sander , Loidl Reinhard , Grewe Benjamin F.
Published: April 2024

1

Studies at the intersection of neuroscience and machine learning have offered new insights to explain hierarchical learning in the neocortex. Two competing hypotheses have emerged: deep learninginspired approximations of the backpropagation algorithm, where neurons adjust synapses to minimize the error, and target learning algorithms, where neurons learn by reducing the feedback needed to achieve a desired activity. Despite decades of research and theoretical arguments supporting either possibility, there is currently no conclusive evidence for either hypothesis. We address this long-standing question by focusing on the relationship between synaptic plasticity and the somatic activity of pyramidal neurons. We first build a pyramidal neuron model integrating subcellular processes including calcium dynamics, backpropagating action potentials, and plateau potentials. Our model predicts that apical synaptic inputs drive basal synaptic plasticity through somatic depolarization caused by plateau potentials. We then test this prediction through in vitro electrophysiology experiments in which we co-stimulate apical and basal synapses to induce basal plasticity. These results allow us to derive distinct predictions for both the target learning and backpropagation hypotheses which we test on in vivo neuronal activity data from the mouse visual cortex. Our findings reveal that cortical learning is consistent with target learning, but not backpropagation, highlighting a critical discrepancy between deep learning and hierarchical learning in the neocortex.