bluuebunny/crossref_metadata_2025 huggingface dataset:
Optic Nerve Sheath Fenestration: A Retrospective Review of Its Safety, Efficacy, and Impact on Optical Coherence Tomography
Authors: Gupta Lalita , Vora Paras , Benningfield Max , Altman Emily A. , Sudhakar Padmaja , Timoney Peter J.
Published: October 2024

Purpose:

This study aimed to evaluate the safety and efficacy of optic nerve sheath fenestration using visual acuity, perimetry, and optical coherence tomography.

Methods:

A retrospective review of patients who underwent an optic nerve sheath fenestration at an academic center between 2016 and 2021 was performed with institutional review board approval. Outcome measures included visual acuity, perimetric mean deviation, optic disc edema grade, improvement in symptoms, and intraoperative and postoperative complications. Optical coherence tomography data collected included macular ganglion cell volume and thickness, as well as retinal nerve fiber layer thickness. Preoperative baseline data and 1-, 6-, and 12-month postoperative data were collected. Repeated measures with a mixed-effects model were used for continuous data, and linear regression analyses were performed.

Results:

A total of 55 patients (86 eyes) underwent optic nerve sheath fenestration, via a medial transconjunctival approach by the same orbital surgeon. After 12-month follow-up, visual acuity (P < 0.05), perimetric mean deviation (P < 0.05), and optic disc edema (P < 0.001) improved in the operative eye. Retinal nerve fiber layer thickness decreased from a mean of 165 to 92 µm (P < 0.001). Macular ganglion cell volume was found to have a small decrease from baseline and correlated well with visual acuity, contrast sensitivity testing, and perimetric mean deviation (P < 0.001).

Conclusions:

Optic nerve sheath fenestration performed via a medial transconjunctival approach is a safe and effective method to preserve vision in patients with papilledema, particularly in cases of fulminant or progressive idiopathic intracranial hypertension. Quantitative measurements of the macular ganglion cell layer can serve as a useful adjunct to other diagnostic testing.
The importance of equity in transplant oncology
Authors: Kodali Sudha , Brombosz Elizabeth W. , Abdelrahim Maen , Mobley Constance M.
Published: October 2024

Purpose of review

Transplant oncology encompasses and utilizes liver transplantation (LT) in combination with other aspects of cancer care to offer improved long-term outcomes for patients with liver cancer, but not all patients have equal access and ability to undergo LT. Social determinants of health may negatively impact a patient's ability to receive liver-related oncologic care, including LT. This review highlights recent work exposing gaps in access to LT, including transplant oncology, and interventions to ameliorate these disparities.

Recent findings

Members of racial and ethnic minorities and indigenous groups, females, socioeconomically disadvantaged persons, and patients from rural areas are less likely to undergo LT. Recent studies have also described programs that have successfully mitigated some of the barriers in access to transplant oncology that these patients experience, including targeted outreach programs and access to virtual healthcare.

Disparities in access to LT for liver cancer are increasingly well described, but additional research is needed to find effective ways to ameliorate these differences.
Spindle Cell Neoplasm With a Novel MN1::TAF3 Fusion: A Rare Case in a Toddler
Authors: White Jesse , Becktell Kerri , Hopp Amanda , Liberio Nicole , Liu Yajuan J. , Hadjiev Jennifer
Published: October 2024

Spindle cell tumors in the pediatric population are uncommonly reported. This case discusses an 18-month-old who presented initially with unilateral ptosis and was found to have an orbital spindle cell tumor. Pathology evaluation of the tissue was extensive with nonspecific morphologic and immunohistochemical features. Molecular testing demonstrated an MN1::TAF3 fusion on RNA sequencing, which has not been previously described in the literature in association with spindle cell neoplasms. This case highlights the challenging nature of classifying and treating a tumor with a novel fusion.
Understanding the multidimensionality of a concern for falling in people with unilateral transtibial amputation: a cross-sectional study
Authors: Nugent Kristin , Viana Ricardo , Payne Michael W. , Unger Janelle , Hunter Susan W.
Published: October 2024

People with lower limb loss often experience psychological concerns related to falling. A concern for falling (CFF) includes four subdomains: fear of falling, self-efficacy, consequences of falling, and perceptions of falls. Limited research exists on how these subdomains are influenced by clinical factors and falls history. This cross-sectional online survey evaluated: (1) associations among CFF outcome measures; (2) relationships between falls history and outcome measures; and (3) clinical and demographic factors related with outcome measures. Inclusion criteria: ≥18 years old, unilateral transtibial amputation and ambulating with a prosthesis. Eight measures assessed CFF: visual analog scale fear of falling, Modified Survey of Activities and Fear of Falling in the Elderly (mSAFFE), Activities-specific Balance Confidence (ABC), Falls Efficacy Scale International (FES-I), Prosthetic Limb Users Survey – Mobility (PLUS-M), Locomotor Capabilities Index, Consequences of Falling Scale, and Perceived Ability to Manage Falls. Pearson bivariate correlation analysis assessed associations among outcome measures. T tests evaluated the association of falls status on outcome scores. Multiple linear regression modelled the clinical and demographic factors related to each measure. Sixty-eight adults (mean 61.8 ± 12.0) participated. Moderate statistically significant (P < 0.001) correlations were found across most outcome measures, with the strongest between PLUS-M and mSAFFE (r = −0.841), and ABC and FES-I (r = −0.821). Faller status was not associated with any measure (P > 0.05). Quality of life was associated with fear of falling, activity avoidance, self-efficacy, and certainty to managing falls (R
2 ranged from 0.27 to 0.47). CFF should be evaluated independently of falls history.
A computational approach to selective attention in embodied approaches to cognitive archaeology
Authors: Constant Axel , Desirèe Di Paolo Laura , Guénin-Carlut Avel , M. Martinez Luis , Criado-Boado Felipe , Müeller Johannes , Clark Andy
Published: October 2024

This article proposes a novel computational approach to embodied approaches in cognitive archaeology called computational cognitive archaeology (CCA). We argue that cognitive archaeology, understood as the study of the human mind based on archaeological findings such as artefacts and material remains excavated and interpreted in the present, can benefit from the integration of novel methods in computational neuroscience interested in modelling the way the brain, the body and the environment are coupled and parameterized to allow for adaptive behaviour. We discuss the kind of tasks that CCA may engage in with a narrative example of how one can model the cumulative cultural evolution of the material and cognitive components of technologies, focusing on the case of knapping technology. This article thus provides a novel theoretical framework to formalize research in cognitive archaeology using recent developments in computational neuroscience.
Rational design and microwave-promoted synthesis of triclosan-based dimers: targeting InhA for anti-mycobacterial profiling
Authors: ­Shekhar ­ , Roquet-Banères Francoise , Anand Amit , Kremer Laurent , Kumar Vipan
Published: October 2024

A set of alkyl-/1H-1,2,3-triazole-based dimers was strategically designed and synthesized to evaluate their
in vitro
anti-mycobacterial activities against
Mycobacterium tuberculosis
and the non-tuberculous
Mycobacterium abscessus
strains. Systematic variations in the nature (alkyl/1H-1,2,3-triazole) and positioning of the linker were implemented based on the docking scores observed in the binding sites identified in the crystal structures of InhA from
M. tuberculosis
and
M. abscessus
. However, the
in vitro
evaluation results revealed that the synthesized compounds did not exhibit inhibitory effects on the growth of mycobacteria, even at the highest tested concentrations. The elevated lipophilicity values determined through ADMET studies for these synthesized dimers might be a contributing factor to their poor activity profiles.
Complete sequences of pIJ101-based Streptomyces-E. coli shuttle vectors
Authors: Brown Katelyn Victoria , Nybo Stephen Eric
Published: October 2024

High-copy number plasmids are indispensable tools for gene overexpression studies in prokaryotes to engineer pathways or probe phenotypes of interest. The development of genetic tools for the industrially-relevant Actinobacteria is of special interest, given their utility in producing keratolytic enzymes and biologically active natural products.Within the Actinobacteria, Streptomyces-Escherichia coli shuttle vectors based on the SCP2* and pIJ101 incompatibility groups are widely employed for molecular cloning and gene expression studies. Here, the sequences of two commonly used pIJ101-based Streptomyces-E. coli shuttle vectors, pEM4 and pUWL201, were determined using next-generation sequencing. These plasmids drive the expression of heterologous genes using the constitutive ermE*p promoter. pEM4 was found to be 8.3 kbp long, containing a β-lactamase gene, thiostrepton resistance marker, the lacZɑ fragment, a ColE1 origin of replication, and the Streptomyces pIJ101 origin of replication. pUWL201 was found to be 6.78 kbp long, containing a β-lactamase gene, thiostrepton resistance marker, the lacZɑ fragment, an ColE1 origin of replication, and the Streptomyces pIJ101 origin of replication. Interestingly, the sequences for both pEM4 and pUWL201 exceed their previously reported size by 1.1 kbp and 0.4 kbp, respectively. This report updates the literature with the corrected sequences for these shuttle vectors, ensuring their compatibility with modern synthetic biology cloning methodologies.
Multi-site analysis of biosynthetic gene clusters from the periodontitis oral microbiome
Authors: Koohi-Moghadam Mohamad , Watt Rory M. , Leung W. Keung
Published: October 2024

Background. Bacteria significantly influence human health and disease, with bacterial biosynthetic gene clusters (BGCs) being crucial in the microbiome–host and microbe–microbe interactions.

Gap statement. Despite extensive research into BGCs within the human gut microbiome, their roles in the oral microbiome are less understood.

Aim. This pilot study utilizes high-throughput shotgun metagenomic sequencing to examine the oral microbiota in different niches, particularly focusing on the association of BGCs with periodontitis.

Methodology. We analysed saliva, subgingival plaque and supragingival plaque samples from periodontitis patients (n=23) and controls (n=16). DNA was extracted from these samples using standardized protocols. The high-throughput shotgun metagenomic sequencing was then performed to obtain comprehensive genetic information from the microbial communities present in the samples.

Results. Our study identified 10 742 BGCs, with certain clusters being niche-specific. Notably, aryl polyenes and bacteriocins were the most prevalent BGCs identified. We discovered several ‘novel’ BGCs that are widely represented across various bacterial phyla and identified BGCs that had different distributions between periodontitis and control subjects. Our systematic approach unveiled the previously unexplored biosynthetic pathways that may be key players in periodontitis.

Conclusions. Our research expands the current metagenomic knowledge of the oral microbiota in both healthy and periodontally diseased states. These findings highlight the presence of novel biosynthetic pathways in the oral cavity and suggest a complex network of host–microbe and microbe–microbe interactions, potentially influencing periodontal disease. The BGCs identified in this study pave the way for future investigations into the role of small-molecule-mediated interactions within the human oral microbiota and their impact on periodontitis.
Effects of Isocaloric Early vs. Late Time-Restricted Eating on Insulin Sensitivity, Cardiometabolic Health, and Internal Circadian Time in Women with Overweight or Obesity: A Randomized Clinical Trial
Authors: Peters Beeke , Schwarz Julia , Schuppelius Bettina , Ottawa Agnieszka , Koppold Daniela A , Weber Daniela , Steckhan Nico , Mai Knut , Grune Tilman , Pfeiffer Andreas F.H. , Michalsen Andreas , Kramer Achim , Pivovarova-Ramich Olga
Published: October 2024

IMPORTANCE It is unclear whether time-restricted eating (TRE) induces cardiometabolic benefits independently of the reduction in calorie intake and whether its effects depend on the timing of the eating window. OBJECTIVE The main objective was to determine whether 8-hour TRE alters insulin sensitivity in an isocaloric setting. The secondary objective was to compare effects of early (eTRE) vs. late TRE (lTRE) on cardiometabolic outcomes and internal circadian time. DESIGN, SETTING, AND PARTICIPANTS The study was a randomized 10-week crossover trial conducted at the German Institute of Human Nutrition Potsdam-Rehbruecke, Germany, between March 2020 to December 2021. Participants were non-diabetic women with overweight or obesity, aged 18 to 70 years. INTERVENTIONS All participants underwent two 2-week isocaloric interventions with a restriction of the eating period to 8 hours: (i) early in the day (eTRE: 8:00-16:00 hr) and (ii) late in the day (lTRE: 13:00-21:00 hr). MAIN OUTCOMES AND MEASURES The primary outcome was insulin sensitivity assessed by an oral glucose tolerance test. Secondary outcomes included levels of glucose, lipids, adipokines, cytokines, oxidative stress markers, and internal circadian phase. RESULTS 31 female participants (mean (SD) BMI of 30.5 (2.9) and median [IQR] age of 62 [53-65] years) completed the trial. Timely adherence was 96.5 % in eTRE and 97.7 % in lTRE. Food records showed a minor daily calorie deficit in eTRE (-167 kcal) but not in lTRE. Insulin sensitivity did not differ between eTRE and lTRE (-0.07; 95% CI, -0.77 to 0.62, P = .83) and showed no within-intervention changes (eTRE: 0.31; 95% CI, -0.14 to 0.76, P = .11; lTRE: 0.19; 95% CI, -0.22 to 0.60, P = .25). 24-hour glucose levels, lipid, inflammatory, and oxidative stress markers showed no clinically meaningful between- and within-intervention differences. lTRE delayed the circadian phase in blood monocytes (24 min; 95% CI, -5 to 54 min, P = .10) and sleep midpoint (15 min; 95% CI, 7 to 22 min, P = .001) compared to eTRE. CONCLUSIONS AND RELEVANCE In a nearly isocaloric setting, neither eTRE nor lTRE improve insulin sensitivity or other cardiometabolic traits despite significant changes in the circadian system.
A Comprehensive Pangenome Approach to Exploring the Probiotic Potential ofWeissella Confusa
Authors: Hossain Md. Saddam , Tuli Shanjana Rahman , Fatima Nigar , Ali Sobur , Moon Shovan Basak , Hashem Abu
Published: October 2024

Background

Fermented foods harbour the bacteriumWeissella confusa, which has probiotic properties but can potentially act as an opportunistic pathogen in humans and animals. Using pangenome analysis, our study aimed to improve the classification and identify functional traits of publicly availableW. confusagenomes, focusing on evaluating their potential as probiotics.

Method

The genomic sequence of 120 strains ofW. confusawas acquired from the NCBI RefSeq database. The downloaded sequences underwent a quality verification and filtering process. Ultimately, the chosen genomes were examined for comparative genomic analysis. We employed Roary to investigate the pangenome ofW. confusa. Fisher’s exact test was utilised to analyse contingency tables, with a significance threshold of p < 0.05 (two-tailed).

Results

Our investigation revealed that the pangenome ofW. confusacomprises 1100 core genes, 184 soft-core genes, 1407 shell genes, and 7006 cloud genes. This finding emphasises the “open” aspect of theW. confusapangenome. The comparison of genomes showed that there were no acquired antibiotic resistance genes. However, the strains had different amounts of prophage regions, CRISPR arrays, and plasmids. Our research identified probiotic marker genes (PMGs), with the majority (78%) found in the core and soft-core genomes of various strains ofW. confusa.

Conclusions

An extensive investigation of theW. confusapangenome has concluded that it could be useful as a probiotic. Additional research is necessary to thoroughly evaluate the potential risks.
Decoding the biogenesis of HIV-induced CPSF6 puncta and their fusion with the nuclear speckle
Authors: Tomasini Chiara , Cuche Celine , Ay Selen , Collard Maxence , Cui Bin , Rashid Mohammad , Bhattacharjee Shaoni , Buchrieser Julian , Luchsinger Charlotte , Bertelli Cinzia , Uversky Vladimir N. , Diaz-Griffero Felipe , Di Nunzio Francesca
Published: October 2024

Viruses rely on host cellular machinery for replication. After entering the nucleus, the HIV genome accumulates in nuclear niches where it undergoes reverse transcription and integrates into neighboring chromatin, promoting high transcription rates and new virus progeny. Despite anti-retroviral treatment, viral genomes can persist in these nuclear niches and reactivate if treatment is interrupted, likely contributing to the formation of viral reservoirs. The post-nuclear entry dynamics of HIV remain unclear, and understanding these steps is critical for revealing how viral reservoirs are established.

In this study, we elucidate the formation of HIV-induced CPSF6 puncta and the domains of CPSF6 essential for this process. We also explore the roles of nuclear speckle scaffold factors, SON and SRRM2, in the biogenesis of these puncta. Through genetic manipulation and depletion experiments, we demonstrate the key role of the intrinsically disordered region of SRRM2 in enlarging nuclear speckles in the presence of the HIV capsid.

We identify the FG domain of CPSF6 as essential for both puncta formation and binding to the viral core, which serves as the scaffold for CPSF6 puncta. While the low-complexity regions (LCRs) modulate CPSF6 binding to the viral capsid, they do not contribute to puncta formation, nor do the disordered mixed charge domains (MCDs) of CPSF6. These results demonstrate how HIV evolved to hijack host nuclear factors, enabling its persistence in the host.

Of note, this study provides new insights into the underlying interactions between host factors and viral components, advancing our understanding of HIV nuclear dynamics and offering potential therapeutic targets for preventing viral persistence.

Highlights

The formation of HIV-induced CPSF6 puncta is critical for restoring HIV-1 nuclear reverse transcription (RT).

CPSF6 protein lacking the FG peptide cannot bind to the viral core, thereby failing to form HIV-induced CPSF6 puncta.

The FG peptide, rather than low-complexity regions (LCRs) or the mixed charge domains (MCDs) of the CPSF6 protein, drives the formation of HIV-induced CPSF6 puncta.

HIV-induced CPSF6 puncta form individually and later fuse with nuclear speckles (NS) via the intrinsically disordered region (IDR) of SRRM2.
Indicators of improved emotion behaviour in 6–14-year-old children following a 4-week placebo controlled prebiotic supplement intervention at home with a parent
Authors: Johnstone Nicola , Kadosh Kathrin Cohen
Published: October 2024

In this double-blind placebo-controlled randomised intervention we investigated the potential benefits of a prebiotic supplement on children’s well-being in a home setting. The primary aim was to determine if this supplement could effectively reduce anxiety, improve mood, and enhance cognitive function, similar to findings in young adults.

Fifty-three healthy children, aged 6 to 14, participated in an 8-week trial. The trial consisted of three testing time points; day zero marked the baseline measurement (T1) followed by a 28-day supplement intervention period during which they consumed 5.5 grams of galactooligosaccharides (GOS) daily under parental guidance. Endline measures (T2) were conducted on the last day of supplement consumption, with a final follow-up testing session (T3) on day 56. Primary outcomes were trait anxiety using a questionnaire and emotional behavior in a dot-probe task on responses to positive and negative images. Secondary outcomes encompassed depression levels, cognitive function tests, and dietary intake recorded in a 4-day food diary. Additionally, we explored whether parents’ emotional behavior had an impact on children’s responses.

While our statistical analysis did not reveal significant effects of GOS, there were noteworthy trends. Trait anxiety levels decreased over time in both groups, with a more pronounced decrease in the GOS group. The GOS group exhibited reduced negative emotional responses compared to the placebo group, and post-trial depression levels decreased in the GOS group over time. Although parental emotional responses correlated with various emotional outcomes in children, they did not influence the intervention effects. In conclusion, these findings suggest positive trends in line with our hypotheses however further investigation with greater statistical power would be beneficial.
Unlocking the potential of wearable device wear time to enhance postpartum depression screening and detection
Authors: Hurwitz Eric , Meltzer-Brody Samantha , Butzin-Dozier Zachary , Patel Rena C. , Elhadad Noémie , Haendel Melissa A.
Published: October 2024

Postpartum depression (PPD) is a mood disorder affecting one in seven women after childbirth that is often under-screened and under-detected. If not diagnosed and treated, PPD is associated with long-term developmental challenges in the child and maternal morbidity. Wearable technologies, such as smartwatches and fitness trackers (e.g., Fitbit), offer continuous and longitudinal digital phenotyping for mood disorder diagnosis and monitoring, with device wear time being an important yet understudied aspect. Using theAll of UsResearch Program (AoURP) dataset, we assessed the percentage of days women with PPD wore Fitbit devices across pre-pregnancy, pregnancy, postpartum, and PPD periods, as determined by electronic health records. Wear time was compared in women with and without PPD using linear regression models. Results showed a strong trend that women in the PPD cohort wore their Fitbits more those without PPD during the postpartum (PPD: mean=72.9%, SE=13.8%; non-PPD: mean=58.9%, SE=12.2%,P-value=0.09) and PPD time periods (PPD: mean=70.7%, SE=14.5%; non-PPD: mean=55.6%, SE=12.9%,P-value=0.08). We hypothesize this may be attributed to hypervigilance, given the common co-occurrence of anxiety symptoms among women with PPD. Future studies should assess the link between PPD, hypervigilance, and wear time patterns. We envision that device wear patterns with digital biomarkers like sleep and physical activity could enhance early PPD detection using machine learning by alerting clinicians to potential concerns facilitating timely screenings, which may have implications for other mental health disorders.
Intestinal parasitic infections associated with nutritional status and inflammatory markers among young children in Huye district, Rwanda
Authors: Twahirwa Wellars , Nyandwi Xavier , Iradukunda Jean D’Amour , Muneza Jean Felix , Kanimba Philbert , Adefaye Khadijat O. , Gahamanyi Noel , Rujeni Nadine
Published: October 2024

Background

Intestinal parasitic infections (IPIs) are a public health issue affecting young children in low and middle income countries (LMICs). These factors may induce malnutrition, as well as systemic and/or intestinal inflammation, depending on the species, intensity of infection, and host response. This study aimed at determining the effect of intestinal parasites on nutritional status and inflammatory responses in pre- and school-aged children in rural areas of the southern province of Rwanda.

Methods

A cross-sectional study involving 127 children under 12 years of age was conducted at two health centers in Huye District, Southern Province, Rwanda, from January to February 2022. A structured questionnaire was used to collect sociodemographic information, feeding habits, anthropometric measurements, and information on infection/malnutrition risk factors. Stool samples were collected to test for intestinal parasites by using microscope, while serum was collected to measure (anti)inflammatory markers [interleukin-10 (IL-10), tumour necrosis factor-alpha (TNF-α), total protein, and C-reactive protein (CRP)].

Results

The overall prevalence of IPIs was 38.6%, with non-pathogenicEntamoeba colibeing the most prevalent (21.3%), followed byAscaris lumbricoides(18.1%),Entamoeba histolytica(11.8%), andTrichuris trichiura(1.6%). Coinfections accounted for 12.6% of the infections. Moreover, 48.0%, 25.2%, and 9.4% of the children were stunted, underweight, and stunted, respectively. Underweight, IL-10, and total protein levels were significantly associated with IPIs. Our findings also indicated that food supplements had a significant positive effect on stunting.

Conclusion

Ascaris lumbricoides,Entamoeba histolytica, andTrichuris trichiurawere the predominant parasites. Intestinal parasitic infections in preschool children and schoolchildren affect the nutritional status, possibly through chronic inflammation. Further mechanistic investigations will shed more light on the regulation of the inflammatory response.
Hospital environments harbor chlorhexidine tolerant bacteria potentially linked to chlorhexidine persistence in the environment
Authors: Shen Jiaxian , Weng Yuhan , Shimada Tyler , Karan Meghana , Watson Andrew , Medernach Rachel L. , Young Vincent B. , Hayden Mary K. , Hartmann Erica M.
Published: October 2024

A One Health approach is essential in combating antibiotic and antimicrobial resistance. Chlorhexidine (di)gluconate (CHG), a widely used antiseptic in medical intensive care units (MICU), has recently come under scrutiny. However, studies on CHG tolerance, particularly in interconnected indoor environments, are limited. We comprehensively explored CHG tolerance in MICU environments from chemical, microbial, and molecular perspectives. Using microcosm experiments and field surveys, we demonstrated that CHG, if transferred from patient skin to environments, can persist on surfaces despite cleaning and disinfection and decrease to sublethal levels for clinically relevant bacteria. We detected widespread CHG-tolerant bacteria (≥ 18.75 µg/mL), including opportunistic pathogens (e.g.,Pseudomonas aeruginosa,Stenotrophomonas maltophilia,Elizabethkingia miricola), with minimum inhibitory concentrations up to 512 μg/mL. Sink drains emerged as critical hotspots, and indoor air as a potential transport mechanism. We observed indications of bacterial persistence, increased tolerance, in-situ evolution, and dissemination across MICU rooms. Molecular analyses revealed heterogeneous and largely unexplored CHG resistance mechanisms and identified resistance determinant candidates, particularlyqacEdelta1-carrying, plasmid-borne multidrug-resistant cassettes. Our findings underscore the importance of understanding human-environment and chemical-microbe interactions to preserve chlorhexidine’s efficacy and inform infection prevention strategies. We advocate for integrated environmental management and clinical interventions under the One Health framework.
Genome report: First whole genome sequence ofTriatoma sanguisuga(Le Conte, 1855), vector of Chagas disease
Authors: Peterson Jennifer K , MacDonald Madolyn , Ellis Vincenzo A.
Published: October 2024

Triatoma sanguisugais the most widespread triatomine bug species in the United States (US). The species vectors the human parasiteTrypanosoma cruzi, which causes Chagas disease. Vector-borne Chagas disease is rarely diagnosed in the US, butT. sanguisugahas been implicated in a handful of cases. Despite its public health importance, little is known about the genomics or population genetics ofT. sanguisuga. Here, we used long-read sequencing to assemble the first whole genome sequence forT. sanguisugausing DNA extracted from one adult specimen from Delaware. The final size of the genome was 1.162 Gbp with 77.7x coverage. The assembly consisted of 183 contigs with an N50 size of 94.97 Kb. The Benchmarking Universal Single-Copy Ortholog (BUSCO) complete score was 99.1%, suggesting a very complete assembly. Genome-wide GC level was 33.56%, and DNA methylation was 18.84%. The genome consists of 61.4% repetitive DNA and 17,799 predicted coding genes. The assembledT. sanguisugagenome was slightly larger than that of Triatominae speciesTriatoma infestansandRhodnius prolixus(949 Mbp with 90.4% BUSCO score and 706 Mbp with 96.5% BUSCO score, respectively). TheT. sanguisugagenome is the first North American triatomine species genome to be sequenced, and it is the most complete genome yet for any Triatominae species. TheT. sangsuigagenome will allow for deeper investigations into epidemiologically relevant aspects of this important vector species, including blood feeding, host seeking, and parasite competence, thus providing potential vector-borne disease management targets and strengthening public health preparedness.
Salmonellaexploits host- and bacterial-derived β-alanine for replication inside host macrophages
Authors: Ma Shuai , Yang Bin , Sun Yuyang , Wang Xinyue , Guo Houliang , Liu Ruiying , Ye Ting , Kang Chenbo , Chen Jingnan , Jiang Lingyan
Published: October 2024

Salmonellais a major foodborne pathogen that can effectively replicate inside host macrophages to establish life-threatening systemic infections.Salmonellamust utilize diverse nutrients for growth in nutrient-poor macrophages, but which nutrients are required for intracellularSalmonellagrowth is largely unknown. Here, we found that either acquisition from the host or de novo synthesis of a nonprotein amino acid, β-alanine, is critical forSalmonellareplication inside macrophages. The concentration of β-alanine is decreased inSalmonella-infected macrophages, while the addition of exogenous β-alanine enhancesSalmonellareplication in macrophages, suggesting thatSalmonellacan uptake host-derived β-alanine for intracellular growth. Moreover, the expression ofpanD,the rate-limiting gene required for β-alanine synthesis inSalmonella,is upregulated whenSalmonellaenters macrophages. Mutation ofpanDimpairedSalmonellareplication in macrophages and colonization in the mouse liver and spleen, indicating that de novo synthesis of β-alanine is essential for intracellularSalmonellagrowth and systemic infection. Additionally, we revealed that β-alanine influencesSalmonellaintracellular replication andin vivovirulence by increasing expression of the zinc transporter genesznuABC,which in turn facilitates the uptake of the essential micronutrient zinc bySalmonella. Taken together, these findings highlight the important role of β-alanine in the intracellular replication and virulence ofSalmonella, andpanDis a promising target for controlling systemicSalmonellainfection.
Role of R5 Pyocin in the Predominance of High-RiskPseudomonas aeruginosaIsolates
Authors: Zhang Liyang , Xu Qi , Tan Filemon C , Deng Yanhan , Hakki Morgan , Shelburne Samuel A. , Kirienko Natalia V.
Published: October 2024

Infections with antimicrobial resistant pathogens, such asPseudomonas aeruginosa,are a frequent occurrence in healthcare settings. HumanP. aeruginosainfections are predominantly caused by a small number of sequence types (ST), such as ST235, ST111, and ST175. Although ST111 is recognized as one of the most prevalent high-riskP. aeruginosaclones worldwide and frequently exhibits multidrug-resistant or extensively drug-resistant phenotypes, the basis for this dominance remains unclear. In this study, we used a genome-wide transposon insertion library screen to discover that the competitive advantage of ST111 strains over certain non-ST111 strains is through production of R pyocins. We confirmed this finding by showing that competitive dominance was lost by ST111 mutants with R pyocin gene deletions. Further investigation showed that sensitivity to ST111 R pyocin (specifically R5 pyocin) is caused by deficiency in the O-antigen ligasewaaL, which leaves lipopolysaccharide (LPS) bereft of O antigen, enabling pyocins to bind the LPS core. In contrast, sensitivity ofwaaLmutants to R1 or R2 pyocins depended on additional genomic changes. In addition, we found the PA14 mutants in lipopolysaccharide biosynthesis (waaL,wbpL,wbpM) that cause high susceptibility to R pyocins also exhibit poor swimming motility. Analysis of 5,135 typedP. aeruginosastrains revealed that several international, high-risk sequence types (including ST235, ST111, and ST175) are enriched for R5 pyocin production, indicating a correlation between these phenotypes and suggesting a novel approach for evaluating risk from emerging prevalentP. aeruginosastrains. Overall, our study sheds light on the mechanisms underlying the dominance of ST111 strains and highlighting the role ofwaaLin extending spectrum of R pyocin susceptibility.
Structural and molecular basis of FAN1 defects in promoting Huntington’s disease
Authors: Li F. , Phadte A. , Bhatia M. , Barndt S. , Monte Carlo A. R. , Hou C-F. D. , Yang R. , Strock S. , Pluciennik A.
Published: October 2024

FAN1 is a DNA dependent nuclease whose proper function is essential for maintaining human health. For example, a genetic variant in FAN1, Arg507 to His hastens onset of Huntington’s disease, a repeat expansion disorder for which there is no cure. How the Arg507His mutation affects FAN1 structure and enzymatic function is unknown. Using cryo-EM and biochemistry, we have discovered that FAN1 arginine 507 is critical for its interaction with PCNA, and mutation of Arg507 to His attenuates assembly of the FAN1-PCNA on a disease-relevant extrahelical DNA extrusions formed within DNA repeats. This mutation concomitantly abolishes PCNA-FAN1-dependent cleavage of such extrusions, underscoring the importance of PCNA to the genome stabilizing function of FAN1. These results unravel the molecular basis for a specific mutation in FAN1 that dramatically hastens the onset of Huntington’s disease.
Striatal cell-type–specific molecular signatures reveal therapeutic targets in a model of dystonia
Authors: Roman Kaitlyn M. , Dinasarapu Ashok R. , Cherian Suraj , Fan Xueliang , Donsante Yuping , Aravind Nivetha , Chan C. Savio , Jinnah H.A. , Hess Ellen J.
Published: October 2024

Striatal dysfunction is implicated in many forms of dystonia, including idiopathic, inherited and iatrogenic dystonias. The striatum is comprised largely of GABAergic spiny projection neurons (SPNs) that are defined by their long-range efferents. Direct SPNs (dSPNs) project to the internal globus pallidus/substantia nigra reticulata whereas indirect pathway SPNs (iSPNs) project to the external pallidum; the concerted activity of both SPN subtypes modulates movement. Convergent results from genetic, imaging and physiological studies in patients suggest that abnormalities of both dSPNs and iSPNs contribute to the expression of dystonia, but the molecular adaptations underlying these abnormalities are not known. Here we provide a comprehensive analysis of SPN cell-type–specific molecular signatures in a model of DOPA-responsive dystonia (DRD mice), which is caused by gene defects that reduce dopamine neurotransmission, resulting in dystonia that is specifically associated with striatal dysfunction. Individually profiling the translatome of dSPNs and iSPNs using translating ribosome affinity purification with RNA-seq revealed hundreds of differentially translating mRNAs in each SPN subtype in DRD mice, yet there was little overlap between the dysregulated genes in dSPNs and iSPNs. Despite the paucity of shared adaptations, a disruption in glutamatergic signaling was predicted for both dSPNs and iSPNs. Indeed, we found that both AMPA and NMDA receptor-mediated currents were enhanced in dSPNs but diminished in iSPNs in DRD mice. The pattern of mRNA dysregulation was specific to dystonia as the adaptations in DRD mice were distinct from those in parkinsonian mice where the dopamine deficit occurs in adults, suggesting that the phenotypic outcome is dependent on both the timing of the dopaminergic deficit and the SPN-specific adaptions. We leveraged the unique molecular signatures of dSPNs and iSPNs in DRD mice to identify biochemical mechanisms that may be targets for therapeutics, including LRRK2 inhibition. Administration of the LRRK2 inhibitor MLi-2 ameliorated the dystonia in DRD mice suggesting a novel target for therapeutics and demonstrating that the delineation of cell-type–specific molecular signatures provides a powerful approach to revealing both CNS dysfunction and therapeutic targets in dystonia.
Unveiling mechanical interactions between cell division and extracellular matrix in human colonic epithelium organoids: A 4D study using DVC
Authors: Magne L. , Pottier T. , Michel D. , Laussu J. , Bonnet D. , Alric L. , Recher G. , Segonds S. , Bugarin F. , Ferrand A.
Published: October 2024

Cell division is a major event in tissue homeostasis, enabling renewal and regeneration. Stem cells, in particular, play an important role in this homeostasis, thanks to their ability to perform symmetric or asymmetric cell divisions. To study cell division, the human colon epithelium represents a model of choice due to its rapid renewal and therefore high proliferative potential. Currently, studying the live mechanical interactions between the epithelium and its matrixin vivois challenging due to the lack of suitable methods. 3D human colon organoids seeded in Matrigel® are good models for this purpose as, from isolated stem cells, they recapitulate the tissue architecture organization and properties. This culture set-up also allows to study the matrix displacements around the organoid.

Here, we studied the impact of cell division within the colonic epithelium on the extracellular matrix. We performed and validated an original experimental and analytical process with a 3D time-lapse confocal microscopy to follow cell mitosis and matrix movements on which we performed Digital Volume Correlation. We showed that these two different types of cell division impact the matrix differently with the asymmetric divisions causing a mainly uniaxial displacement, whereas symmetric ones involved a multiaxial and more important one.
Acute GARP depletion disrupts vesicle transport, leading to severe defects in sorting, secretion, and O-glycosylation
Authors: Khakurel Amrita , Pokrovskaya Irina , Lupashin Vladimir V.
Published: October 2024

The GARP complex is an evolutionarily conserved protein complex proposed to tether endosome-derived vesicles at the trans-Golgi network. While prolonged depletion of GARP leads to severe trafficking and glycosylation defects, the primary defects linked to GARP dysfunction remain unclear. In this study, we utilized the mAID degron strategy to achieve rapid degradation of VPS54 in human cells, acutely disrupting GARP function. This resulted in the partial mislocalization and degradation of a subset of Golgi-resident proteins, including TGN46, ATP7A, TMEM87A, CPD, C1GALT1, and GS15. Enzyme recycling defects led to the early onset of O-glycosylation abnormalities. Additionally, while the secretion of fibronectin and cathepsin D was altered, mannose-6-phosphate receptors were largely unaffected. Partial displacement of COPI, AP1, and GGA coats caused a significant accumulation of vesicle-like structures and large vacuoles. Electron microscopy detection of GARP-dependent vesicles, along with the identification of specific cargo proteins, provides direct experimental evidence of GARP’s role as a vesicular tether. We conclude that the primary defects of GARP dysfunction involve vesicular coat mislocalization, accumulation of GARP-dependent vesicles, degradation and mislocalization of specific Golgi proteins, and O-glycosylation defects.
Computational design of a thermostable de novo biocatalyst for whole cell biotransformations
Authors: Elaily Wael , Stoll David , Chakatok Morakot , Aleotti Matteo , Grill Birgit , Lechner Horst , Hall Melanie , Oberdorfer Gustav
Published: October 2024

Several industrially relevant catalytic strategies have emerged over the last couple of decades, with biocatalysis gaining lots of attention in this respect. However, this type of catalysis would be even more thriving if customizable and stable protein scaffolds would be readily available. Such highly stable protein scaffolds could act as asymmetric reaction chambers in catalyzing a wide range of reactions. In this study, we are detailing the design and experimental characterization of computationally designed de novo proteins with a non-natural fold, which act as biocatalysts. The initial design and several variants of it, catalyze the aldol condensation and the retro-aldol reac-tion. All designs form a helical barrel structure comprised of six antiparallel straight helices con-nected by five loops, resulting in an open channel with two accessible cavities. The designs ex-hibit high thermal stability and an excellent overall fit between measured and calculated scattering profiles from small-angle x-ray scattering experiments. An experimentally determined crystal structure of a surface redesigned variant shows close to perfect agreement to the design model. To highlight the versatility and mutational tolerance of this fold, we rationally designed variants in which the active site is placed at different positions throughout the central channel of the original design. Finally, we showcase that the initial design as well as variants exhibit significant aldolase/retro-aldolase activity in whole cell biotransformations, making them the first de novo bio-catalysts to be tested in this form. With a tolerance of up to 20% of organic solvent, these de-signs hold promise for further utilization and optimization in the field of white biotechnology.
Molecular states underlying neuronal cell type development and plasticity in the whisker cortex
Authors: Butrus Salwan , Monday Hannah R. , Yoo Christopher J. , Feldman Daniel E. , Shekhar Karthik
Published: October 2024

Mouse whisker somatosensory cortex (wS1) is a major model system to study the experience-dependent plasticity of cortical neuron physiology, morphology, and sensory coding. However, the role of sensory experience in regulating neuronal cell type development and gene expression in wS1 remains poorly understood. We assembled and annotated a transcriptomic atlas of wS1 during postnatal development comprising 45 molecularly distinct neuronal types that can be grouped into eight excitatory and four inhibitory neuron subclasses. Using this atlas, we examined the influence of whisker experience from postnatal day (P) 12, the onset of active whisking, to P22, on the maturation of molecularly distinct cell types. During this developmental period, when whisker experience was normal, ∼250 genes were regulated in a neuronal subclass-specific fashion. At the resolution of neuronal types, we found that only the composition of layer (L) 2/3 glutamatergic neuronal types, but not other neuronal types, changed substantially between P12 and P22. These compositional changes resemble those observed previously in the primary visual cortex (V1), and the temporal gene expression changes were also highly conserved between the two regions. In contrast to V1, however, cell type maturation in wS1 is not substantially dependent on sensory experience, as 10-day full-face whisker deprivation did not influence the transcriptomic identity and composition of L2/3 neuronal types. A one-day competitive whisker deprivation protocol also did not affect cell type identity but induced moderate changes in plasticity-related gene expression. Thus, developmental maturation of cell types is similar in V1 and wS1, but sensory deprivation minimally affects cell type development in wS1.

Highlights

-

A single-nucleus transcriptomic atlas of the whisker somatosensory cortex (wS1) during early postnatal development

-

Different neuronal subclasses in wS1 show distinct developmental gene expression changes

-

The composition of L2/3 glutamatergic neurons changes between the second and the third postnatal week

-

Developmental gene expression and cell type changes are conserved between wS1 and the primary visual cortex (V1)

-

Unlike V1, these changes are not affected by prolonged sensory deprivation

-

Brief whisker deprivation induces subclass-specific activity-dependent gene expression in a whisker column-specific fashion
Genetically-encoded markers for confocal visualization of single dense core vesicles
Authors: Yu Junwei , Zhang Yunpeng , Clements Kelsey , Chen Nannan , Griffith Leslie C.
Published: October 2024

Neuronal dense core vesicles (DCVs) store and release a diverse array of neuromodulators, trophic factors and bioamines. The analysis of single DCVs has largely been possible only using electron microscopy, which makes understanding cargo segregation and DCV heterogeneity difficult. To address these limitations, we developed genetically-encoded markers for DCVs that can be used in combination with standard immunohistochemistry and expansion microscopy, to enable single-vesicle resolution with confocal microscopy.
Cholecystokinin-expressing GABA neurons elicit long-term potentiation in the cortical inhibitory synapses and attenuate sound-shock associative memory
Authors: Zhang Ge , Pang Kwok Kin , Chen Xi , Huang Fengwen , He Jufang
Published: October 2024

Neuronal interactions between inhibitory and excitatory neurons play a pivotal role in regulating the balance of excitation and inhibition in the central nervous system (CNS). Consequently, the efficacy of inhibitory/excitatory synapses profoundly affects neural network processing and overall neuronal functions. Here, we describe a novel form of long-term potentiation (LTP) induced at cortical inhibitory synapses and its behavioral consequences. We show that high-frequency laser stimulation (HFLS) of GABAergic neurons elicit inhibitory LTP (i-LTP) in pyramidal neurons of the auditory cortex (AC). The selective activation of cholecystokinin-expressing GABA (GABACCK) neurons is essential for the formation of HFLS-induced i-LTP, rather than the classical parvalbumin (PV) neurons and somatostatin (SST) neurons. Intriguingly, i-LTP can be evoked in the AC by adding the exogenous neuropeptide CCK when PV neurons and SST neurons are selectively activated in PV-Cre and SST-Cre mice, respectively. Additionally, we discovered that low-frequency laser stimulation (LFLS) of PV neurons paired with HFLS of GABACCKneurons potentiates the inhibitory effect of PV interneurons on pyramidal neurons, thereby generating heterosynaptic i-LTP in the AC. Notably, light activation of GABACCKneurons in CCK-Cre mice significantly attenuates sound-shock associative memory, while stimulation of PV neurons does not affect this memory in PV-Cre mice. In conclusion, these results demonstrate a critical mechanism regulating the excitation-inhibition balance and modulating learning and memory in cortical circuits. This mechanism might serve as a potential target for the treatment of neurological disorders, including epilepsy and Alzheimer’s disease.
Subdiffusion of heavy quarks in hot QCD matter by the fractional Langevin equation
Authors: Prakash Jai
Published: October 2024

The subdiffusion phenomena are studied for heavy quarks dynamics in the hot QCD matter. Our approach aims to provide a more realistic description of heavy quark dynamics through detailed theoretical analyses and numerical simulations, utilizing the fractional Langevin equation framework with the Caputo fractional derivative. I present numerical schemes for the fractional Langevin equation for subdiffusion and calculate the time evolution mean squared displacement and mean squared momentum of the heavy quarks. My results indicate that the mean squared displacements of the heavy quarks for the subdiffusion process deviate from a linear relationship with time. Further, I calculate the normalized momentum correlation function, kinetic energy, and momentum spread. Finally, I show the effect of subdiffusion on experimental observables, the nuclear modification factor.

Published by the American Physical Society
2024