bluuebunny/crossref_metadata_2025 huggingface dataset:
The Use of Flap Techniques to Preserve Limb Length in Patients with Transmetatarsal Amputations
Authors: Deldar Romina , Sayyed Adaah A. , Cach Gina , Choi Christopher , Garada Firras , Atves Jayson N. , Steinberg John S. , Fan Kenneth L. , Attinger Christopher E. , Evans Karen K.
Published: June 2023

Background:

Chronic lower extremity (LE) wounds affect up to 13% of the United States population. Transmetatarsal amputation (TMA) is frequently performed in comorbid patients with chronic forefoot wounds. TMA allows limb salvage and preserves functional gait, without need for prosthesis. Traditionally, when tension-free primary closure is not possible, a higher-level amputation is performed. This is the first series to evaluate the outcomes following local and free flap coverage of TMA stumps in patients with chronic foot wounds.

Methods:

A retrospective cohort of patients who underwent TMA with flap coverage from 2015-2021 were reviewed. Primary outcomes included flap success, early postoperative complications, and long-term outcomes (limb salvage and ambulatory status). Patient-reported outcome measures using the lower extremity functional scale (LEFS) were also collected.

Results:

Fifty patients underwent 51 flap (26 local, 25 free flap) reconstructions following TMA. Average age and BMI were 58.5 years and 29.8 kg/m2, respectively. Comorbidities included diabetes (n=43, 86%) and peripheral vascular disease (n=37, 74%). Flap success rate was 100%. At mean follow-up of 24.8 months (range, 0.7 to 95.7 months), the limb salvage rate was 86.3% (n=44). Forty-four patients (88%) were ambulatory. The LEFS survey was completed by 24 surviving patients (54.5%). Mean LEFS score was 46.6 ± 13.9, correlating with 58.2 ± 17.4% of maximal function.

Conclusion:

Local and free flap reconstruction following TMA are viable methods of soft tissue coverage for limb salvage. Applying plastic surgery flap techniques for TMA stump coverage allows for preservation of increased foot length and ambulation without a prosthesis.
Auditory and cognitive function in older adults living with and without HIV
Authors: Torre Peter , Sundermann Erin E. , Brandino Amanda , Heaton Anne , Devore Julia , Anderson Albert M. , Moore Raeanne C.
Published: June 2023

Objectives:

To evaluate: 1) the peripheral hearing sensitivity and central auditory processing in persons living with HIV (PWH) and persons living without HIV (PWoH); and 2) the association between cognitive function and central auditory processing in PWH and PWoH.

Design:

Cross-sectional, observational study.

Methods:

Participants included 67 PWH (70.2% male; mean age = 66.6 years [SD = 4.7 years]) and 35 PWoH (51.4% male; mean age = 72.9 years [SD = 7.0 years]). Participants completed a hearing assessment and a central auditory processing assessment that included dichotic digits testing (DDT). Pure-tone air-conduction thresholds were obtained at octave frequencies from 0.25 through 8 kHz. A pure-tone average (PTA) was calculated from 0.5, 1, 2, and 4 kHz thresholds for each ear. Participants also completed a neuropsychological battery assessing cognition in seven domains.

Results:

PWH had slightly lower (i.e., better) PTAs compared to PWoH, but this was not statistically significant. Conversely, PWH and PWoH had similar DDT results for both ears. Poorer verbal fluency, learning, and working memory performance was significantly related to lower DDT scores, and those defined as having verbal fluency, learning, and working memory impairment had significantly poorer DDT scores (8–18% lower) in both ears.

Conclusions:

Hearing and DDT results were similar in PWH and PWoH. The relationship between verbal fluency, learning, and working memory impairment and poorer DDT results did not differ by HIV serostatus. Clinicians, particularly audiologists, should be mindful of cognitive functioning abilities when evaluating central auditory processing.
The Effect of Precolonoscopy Lavender Inhalation on Patient Anxiety and Comfort
Authors: Sayilan Samet , Sayilan Aylin Aydin , Mert Selda , Öztekin Seher Deniz , Baydemir Canan
Published: June 2023

The purpose of this study was to determine the effect of lavender oil inhalation on the anxiety and comfort levels of patients scheduled for colonoscopy. Seventy-three experimental group patients scheduled for colonoscopy at a training and research hospital in the west of Turkey in June to September 2022 and 72 control group patients were included in this randomized, controlled, prospective study. Minimal sedation (propofol 2–3 mg/kg) was applied in both groups. Lavender inhalation was applied to the experimental group, whereas the control group patients received nursing care (vital sign monitoring, prevention of complications, and rest). The State-Trait Anxiety Inventory and the Shortened General Comfort Questionnaire were used for pre- and postprocedural data collection. Median ages were 53.00 years (47.25–59.00) in the experimental group patients and 51.00 (44.00–59.5) in the control group. Although postprocedural state anxiety scores were lower in the experimental group compared with the control group, the difference was not statistically significant (p = .069). The general postcolonoscopy comfort score was significantly higher in the experimental group compared with the control group (p < .001). Trait anxiety scores also increased as the number of colonoscopies increased in both groups. We conclude that lavender oil inhalation, a simple and inexpensive intervention, increases patient comfort while exhibiting a positive, albeit statistically insignificant, effect on anxiety.
Acinetobacter baumannii ATCC 17978 encodes a microcin system with antimicrobial properties for contact-independent competition
Authors: Bisaro Fabiana , Shuman Howard A. , Feldman Mario F. , Gebhardt Michael J. , Pukatzki Stefan
Published: June 2023

Acinetobacter baumannii

is a multidrug-resistant opportunistic pathogen that persists in the hospital environment and causes various clinical infections, primarily affecting immunocompromised patients.

A. baumannii

has evolved a wide range of mechanisms to compete with neighbouring bacteria. One such competition strategy depends on small secreted peptides called microcins, which exert antimicrobial effects in a contact-independent manner. Here, we report that

A. baumannii

ATCC 17978 (AB17978) encodes the class II microcin 17 978 (Mcc17978) with antimicrobial activity against closely related

Acinetobacter

, and surprisingly, also

Escherichia coli

strains. We identified the genetic locus encoding the Mcc17978 system in AB17978. Using classical bacterial genetic approaches, we determined that the molecular receptor of Mcc17978 in

E. coli

is the iron-catecholate transporter Fiu, and in

Acinetobacter

is Fiu’s homolog, PiuA. In bacteria, the Ferric uptake regulator (Fur) positively regulates siderophore systems and microcin systems under iron-deprived environments. We found that the Mcc17978 system is upregulated under low-iron conditions commonly found in the host environment and identified a putative Fur binding site upstream of the mcc17978 gene. When we tested the antimicrobial activity of Mcc17978 under different levels of iron availability, we observed that low iron levels not only triggered transcriptional induction of the microcin, but also led to enhanced microcin activity. Taken together, our findings suggest that

A. baumannii

may utilize microcins to compete with other microbes for resources during infection.
PICNIC accurately predicts condensate-forming proteins regardless of their structural disorder across organisms
Authors: Hadarovich Anna , Singh Hari Raj , Ghosh Soumyadeep , Rostam Nadia , Hyman Anthony A. , Toth-Petroczy Agnes
Published: June 2023

Biomolecular condensates are membraneless organelles that can concentrate hundreds of different proteins to operate essential biological functions. However, accurate identification of their components remains challenging and biased towards proteins with high structural disorder content with focus on self-phase separating (driver) proteins. Here, we present a machine learning algorithm, PICNIC (Proteins Involved in CoNdensates In Cells) to classify proteins involved in biomolecular condensates regardless of their role in condensate formation. PICNIC successfully predicts condensate members by identifying amino acid patterns in the protein sequence and structure in addition to the intrinsic disorder and outperforms previous methods. We performed extensive experimental validationin celluloand demonstrated that PICNIC accurately predicts 21 out of 24 condensate-forming proteins regardless of their structural disorder content. Even though increasing disorder content was associated with organismal complexity, we found no correlation between predicted condensate proteome content and disorder content across organisms. Overall, we applied a novel machine learning classifier to interrogate condensate components at single protein and whole-proteome levels across the tree of life (picnic.cd-code.org).
A Deep Learning Approach for Mental Health Quality Prediction Using Functional Network Connectivity and Assessment Data
Authors: Ajith Meenu , Aycock Dawn M. , Tone Erin B. , Liu Jingyu , Misiura Maria B. , Ellis Rebecca , King Tricia Zawacki , Dotson Vonetta M. , Calhoun Vince
Published: June 2023

While one can characterize mental health using questionnaires, such tools do not provide direct insight into the underlying biology. By linking approaches that visualize brain activity to questionnaires in the context of individualized prediction, we can gain new insights into the biology and behavioral aspects of brain health. Resting-state fMRI (rs-fMRI) can be used to identify biomarkers of these conditions and study patterns of abnormal connectivity. In this work, we estimate mental health quality for individual participants using static functional network connectivity (sFNC) data from rs-fMRI. The deep learning model uses the sFNC data as input to predict four categories of mental health quality and visualize the neural patterns indicative of each group. We used guided gradient class activation maps (guided Grad-CAM) to identify the most discriminative sFNC patterns. The effectiveness of this model was validated using the UK Biobank dataset, in which we showed that our approach outperformed four alternative models by 4-18% accuracy. The proposed model’s performance evaluation yielded a classification accuracy of 76%, 78%, 88%, and 98% for the excellent, good, fair, and poor mental health categories, with poor mental health accuracy being the highest. The findings show distinct sFNC patterns across each group. The patterns associated with excellent mental health consist of the cerebellar-subcortical regions, whereas the most prominent areas in the poor mental health category are in the sensorimotor and visual domains. Thus the combination of rs-fMRI and deep learning opens a promising path for developing a comprehensive framework to evaluate and measure mental health. Moreover, this approach had the potential to guide the development of personalized interventions and enable the monitoring of treatment response. Overall this highlights the crucial role of advanced imaging modalities and deep learning algorithms in advancing our understanding and management of mental health.
Boldine alters serum lipidomic signatures after acute spinal cord transection in male mice
Authors: Graham Zachary A. , Siedlik Jacob A. , Toro Carlos A. , Harlow Lauren , Cardozo Christopher P.
Published: June 2023

Traumatic spinal cord injury (SCI) results in wide-ranging cellular and systemic dysfunction in the acute and chronic time frames after the injury. Chronic SCI has well-described secondary medical consequences while acute SCI has unique metabolic challenges as a result of physical trauma, in-patient recovery and other post-operative outcomes. Here, we used high resolution mass spectrometry approaches to describe the circulating lipidomic and metabolomic signatures using blood serum from mice 7 d after a complete SCI. Additionally, we probed whether the aporphine alkaloid, boldine, was able to prevent SCI-induced changes observed using these ‘omics platforms. We found that SCI resulted in large-scale changes to the circulating lipidome but minimal changes in the metabolome, with boldine able to reverse or attenuate SCI-induced changes in the abundance of 50 lipids. Multiomic integration using xMWAS demonstrated unique network structures and community memberships across the groups.
Bench-ML: A Benchmarking Web Interface for Machine Learning Methods and Models in Genomics
Authors: Rene Lopez , Mario Makita , Laura Ortega , Avantika Lal , Hernan De La Garza
Published: June 2023

Machine learning is a complex but essential technology in genomics data analysis and its popularity has increased the rate of new methodological approaches published but this raises the question of how models should be benchmarked and validated.

Bench-ML is a generalizable and easy to use web interface for benchmarking and validation that can preprocess data, train, test, evaluate and compare machine learning algorithms for genomics. It makes benchmarking machine learning methods more accessible by enabling genomics scientists to perform end-to-end analyses, visualize results and evaluate performance or metrics to compare methods and models by providing a point of reference using only a web browser.

To improve something it needs to be measured; To benchmark and evaluate models Bench-ML provides several strategies, methodologies, and tools to generate measurements and visualizations to track experiments to help identify areas of opportunity using metrics such as loss and accuracy, model visualization, learning and saturation curves, principal component analysis, feature scoring, confusion matrix, regression for training and test data, mean absolute error, etc.

Bench-ML explains the different options to test and validate machine and deep learning models to identify problematic areas and potentially improve performance. Bench-ML provides several strategies to improve performance like showing when a model is not performing or when different hyperparameters values could be needed, it also helps fine tune hyperparameter values and to identify accuracy across multiple classes and from these classes which class could affect performance.

The selection, development, and comparison of machine learning methods and models in genomics datasets can be a daunting task based on the goals of a particular study or the target problem. Machine learning is very good at pattern recognition but modeling the world is much more than that so how to know if a machine learning method or model is performing at a good sensitivity and specificity in large genomics datasets is still a big problem and this is where Bench-ML can help.
PTP1B phosphatase puts a brake on iPSC-derived neutrophil motility and antimicrobial function
Authors: Giese Morgan A. , Bennin David A. , Schoen Taylor J. , Peterson Ashley N. , Brand Josh , Jung Ho Sun , Dinh Huy Q. , Slukvin Igor I. , Huttenlocher Anna
Published: June 2023

Neutrophils are rapidly recruited to sites of infection and are critical for pathogen clearance. Neutropenic patients are at high risk for fungal and bacterial infections and can benefit from granulocyte transfusion therapy. Human induced pluripotent stem cells (iPSCs) could provide a robust source of neutrophil-like cells for infusion as they can be generated in large quantities and do not require a donor. However, dampened intracellular signaling limits their cellular activation and response. Here, we show that we can engineer iPSC-derived neutrophils (iNeutrophils) for enhanced motility and anti-microbial functions. Deletion of the PTP1B phosphatase increased iNeutrophil PI3K and ERK signaling and was associated with increased F-actin polymerization, cell migration and phagocytosis. PTP1B deletion also increased production of inflammatory cytokines, including the neutrophil chemoattractant IL-8. Furthermore, PTP1B-KO iNeutrophils displayed a highly activated morphology and were more responsive to the fungal pathogenAspergillus fumigatus. KO iNeutrophils efficiently migrated to and swarmed hyphae resulting in inhibition of fungal growth. Taken together, deletion of the PTP1B phosphatase removes the “brakes” on iPSC-derived intracellular signaling and neutrophil function.

Key points

Deletion of PTP1B increases iPSC-derived neutrophil intracellular signaling to improve motility and phagocytosis.

Deletion of PTP1B enhances iPSC-derived neutrophil swarming response and ability to inhibit fungal growth.
Environmental variability can promote parasite diversity within hosts and transmission among hosts
Authors: Jarvis-Cross Madeline , Krkosek Martin
Published: June 2023

While the mechanisms that govern disease emergence and spread among hosts are increasingly well-described, the mechanisms that promote parasite diversity within-hosts, affecting host outcomes and spillover potential, have been comparatively understudied. Furthermore, while attention has been paid to the effects of increasing temperatures on disease systems, the effects of environmental variability have been left underexplored, despite rising climatic variability. To investigate the impacts of environmental variability on parasite diversity within-hosts, we analyzed a model of within-host population dynamics wherein two parasites indirectly compete through the host’s immune response. We simulated the model under constant, demographically stochastic, environmentally stochastic, and demographically and environmentally stochastic conditions, and analysed the viability and longevity of non-equilibrium parasite co-occurrence. We found that environmental stochasticity increased the viability and longevity of parasite co-occurrence, suggesting that thermal variability arising from climatic change and as a physiological trait may promote parasite diversity within ectotherms and help explain bats’ propensity to support diverse communities of parasites. Further, we found that under certain conditions, the transmissibility of co-occurring parasites can surpass the transmissibility of single parasites, suggesting that thermal variability may increase the transmissibility of co-occurring parasites.
Electrocatalytic on-site oxygenation for transplanted cell-based-therapies
Authors: Lee Inkyu , Surendran Abhijith , Fleury Samantha , Gimino Ian , Curtiss Alexander , Fell Cody , Shiwarski Daniel , El-Refy Omar , Rothrock Blaine , Jo Seonghan , Schwartzkopff Tim , Mehta Abijeet Singh , John Sharon , Ji Xudong , Nikiforidis Georgios , Feinberg Adam , Hester Josiah , Weber Douglas J. , Veiseh Omid , Rivnay Jonathan , Karni Tzahi Cohen-
Published: June 2023

Implantable cell therapies and tissue transplants require sufficient oxygen supply to function and are limited by a delay or lack of vascularization from the transplant host1, 2. Exogenous oxygen production can support cells and tissues, such as pancreatic islets and engineered therapeutic cells. Previous oxygenation strategies have targeted gas circulation or decomposition of solid peroxides. These strategies however require bulky implants, transcutaneous supply lines, and are limited in their total oxygen production or regulation3, 4. Readily integrated and controlled production of oxygen has eluded cell therapy devices. Here, we show an electrocatalytic approach that enables bioelectronic control of oxygen generation in complex cellular environments to sustain engineered cell viability and therapy production under hypoxic stress and at high cell densities. Nanostructured sputtered iridium oxide serves as an ideal catalyst for oxygen evolution reaction (OER) at neutral pH. It enables a lower OER onset and shows selective oxygen production without evolution of toxic side products over a 300 mV window of operation. This electrocatalytic on site oxygenator (ecO2) can sustain high cell loadings (>60k cells/mm3) in hypoxic conditions in vitro and in vivo. Our results demonstrate that exogenous oxygen production devices can be readily integrated into bioelectronic platforms and enable high cell loadings in smaller device footprints with broad applicability.
The Multifaceted Effects of Short-Term Acute Hypoxia Stress: Insights into the tolerance mechanism ofPropsilocerus akamusi(Diptera: Chironomidae)
Authors: Zhang Yao , Zhang Qing-Ji , Xu Wen-Bin , Zou Wei , Xiang Xian-Ling , Gong Zhi-Jun , Cai Yong-Jiu
Published: June 2023

Plenty of freshwater species, especially macroinvertebrates that are essential to the provision of numerous ecosystem functions, encountered higher mortality due to acute hypoxia. However, within the family Chironomidae, a wide range of tolerance to hypoxia/anoxia is displayed andPropsilocerus akamusidepends on this great endurance to become a dominant species in eutrophic lakes. To further understand howP. akamusiresponds to acute hypoxic stress, we used multi-omics analysis in combination with histomorphological characteristics and physiological indicators. To evaluate enzyme activity, the transcriptome and metabolome, and histomorphological characteristics, we set up two groups: a control group (DO 8.4mg/L) and a hypoxic group (DO 0.39mg/L). With blue-black chromatin, cell tightness, cell membrane invagination, and the production of apoptotic vesicles, tissue cells displayed typical apoptotic features. While lactate dehydrogenase (LDH), (Alcohol dehydrogenase) ADH, catalase (CAT), and Na+/K+ -ATPase (NKA) activities were dramatically enhanced under hypoxic stress, glycogen content, and superoxide dismutase (SOD) activities were significantly reduced compared to the control group. The above results were further supported by the joint analysis of the transcriptome and metabolome, which further revealed that in addition to carbohydrates, including glycogen, the energy metabolism of the fatty acid, trehalose, and glyoxylate cycles is also included. Furthermore, we also revealed the ethanol tested in hypoxic stress should derive from symbiodinium ofP akamusi.Understanding the processes which enableP. akamusito survive lengthy periods of hypoxia in eutrophic lakes might help to design sensitive biomonitoring procedures, and this species has the potential to be used as an effective eutrophication indicator.
Single Nuclei RNA Sequencing of the Gastrocnemius Muscle in Peripheral Artery Disease
Authors: Pass Caroline , Palzkill Victoria , Tan Jianna , Kim Kyoungrae , Thome Trace , Yang Qingping , Fazzone Brian , Robinson Scott T. , O’Malley Kerri A. , Yue Feng , Scali Salvatore T. , Berceli Scott A. , Ryan Terence E.
Published: June 2023

Background

Lower extremity peripheral artery disease (PAD) is a growing epidemic with limited effecOve treatment options. Herein, we provide a single nuclei atlas of PAD limb muscle to facilitate a better understanding of the composition of cells and transcriptional differences that comprise the diseased limb muscle.

Methods

We obtained gastrocnemius muscle specimens from 20 PAD patients and 12 non-PAD controls. Nuclei were isolated and single nuclei RNA sequencing (snRNAseq) was performed. The composition of nuclei was characterized by iteraOve clustering via principal component analysis, differenOal expression analysis, and the use of known marker genes. BioinformaOcs analysis was performed to determine differences in gene expression between PAD and non-PAD nuclei, as well as subsequent analysis of intercellular signaling networks. Additional histological analyses of muscle specimens accompany the snRNAseq atlas.

Results

snRNAseq analysis indicated a fiber type shim with PAD paOents having fewer Type I (slow/oxidaOve) and more Type II (fast/glycolyOc) myonuclei compared to non-PAD, which was confirmed using immunostaining of muscle specimens. Myonuclei from PAD displayed global upregulation of genes involved in stress response, autophagy, hypoxia, and atrophy. Subclustering of myonuclei also idenOfied populations that were unique to PAD muscle characterized by metabolic dysregulation. PAD muscles also displayed unique transcriptional profiles and increased diversity of transcriptomes in muscle stem cells, regeneraOng myonuclei, and fibro-adipogenic progenitor (FAPs) cells. Analysis of intercellular communication networks revealed FAPs as a major signaling hub in PAD muscle, as well as deficiencies in angiogenic and bone morphogeneOc protein signaling which may contribute to poor limb function in PAD.

Conclusions

This reference snRNAseq atlas provides a comprehensive analysis of the cell composition, transcriptional signature, and intercellular communication pathways that are altered in the PAD condition.
Tissue-bound hyaluronan molecular weight as a regulator of dendritic cell immune potency
Authors: Quartey Brian Chesney , Sapudom Jiranuwat , ElGindi Mei , Alatoom Aseel , Teo Jeremy
Published: June 2023

Hyaluronic acid (HA) is a major glycosaminoglycan found in the extracellular matrix (ECM) and exhibits immunoregulatory properties depending on its molecular weight (MW). However, the impact of tissue bound HA on dendritic cell (DC) functions is not well understood due to the varying distribution of HA MW under different physiological and pathological conditions. To investigate DCs in defined biosystems, we used three-dimensional (3D) collagen matrices modified with HA of specific MW, while maintaining similar microstructure and HA levels. Using these matrices, we examined the influence of HA on cytokine binding and observed distinct properties depending on the presence and MW of HA, suggesting modulation of cytokine availability by the different MW of HA. Our studies on DC immune potency revealed that low molecular weight HA (LMW-HA; 8-15 kDa) enhances immature DC (iDC) differentiation and antigen uptake, while medium (MMW-HA; 500-750 kDa) and high molecular weight HA (HMW-HA; 1250-1500 kDa) increase cytokine secretion in matured DCs (mDCs). Interestingly, the modulation of DCs surface marker expression and cytokine secretion by different MW of HA appeared to be independent of CD44. However, we found that cytokine secretion of DCs was dependent on the CD44 receptor regardless of the presence or absence of HA in the matrix. Additionally, we observed reduced migratory capacity of iDCs and mDCs when cultured on MMW- and HMW-HA matrices, and this effect was dependent on CD44. In summary, our findings provide new insights into the MW-dependent effects of tissue-bound HA on DCs, opening avenues for the design of DC-modulating materials to enhance DC-based therapy.
Iron Oxide Nanoparticles Coated with Biodegradable Block-Copolymer PDMAEMA-b-PMPC and Functionalized with Aptamer for HER2 Breast Cancer Cell Identification
Authors: de Valega Negrão Cyro von Zuben , Cerize Natália Neto Pereira , Justo-Junior Amauri da Silva , Liszbinski Raquel Bester , Meneguetti Giovanna Pastore , Araujo Larissa , Rocco Silvana Aparecida , Gonçalves Kaliandra de Almeida , Cornejo Daniel Reinaldo , Leo Patrícia , Perecin Caio , Adamoski Douglas , Dias Sandra Martha Gomes
Published: June 2023

Hybrid nanoparticles have shown promise in biomedical applications; however, their seamless integration into clinical settings remains challenging. Here, we introduce a novel metal oxide polymer hybrid nanoparticle (NP) with a high affinity for nucleic acids. Iron oxide nanoparticles (IONP) were initially synthesized via the co-precipitation method and subjected to comprehensive characterization. Subsequently, block copolymers were synthesized using the Reversible Addition−Fragmentation Chain Transfer (RAFT) technique, employing the zwitterionic PMPC (Poly (2 Methacryloyloxyethyl Phosphorylcholine)) and the cationic PDMAEMA (Poly(2 (Dimethylamino) Ethyl Methacrylate)) with varying degrees of polymerization. In vitro cytotoxicity studies demonstrated the biocompatibility of the synthesized nanoparticles, with no observed toxicity up to a concentration of 150 µg/mL. The cationic polymer PDMAEMA facilitated the facile coating of IONP, forming the IONPP complex, consisting of a 13.27 metal core and a 3.1 nm block-copolymer coating. Subsequently, the IONPP complex was functionalized with a DNA aptamer specifically targeting the human epidermal growth factor receptor 2 (HER2) in breast cancer, forming IONPPP. The block-copolymer exhibited an EC50of 7.07 µg/mL and demonstrated enhanced recognition efficiency in HER2-amplified SKBR3 cells. Our study presents a comprehensive IONPPP characterization capable of binding short DNA sequences and targeting proteins such as HER2. This newly developed nanoparticle holds significant potential for cancer cell identification and isolation, offering promising prospects in cancer research and clinical applications.

1.

Statement of significance

Despite recent advancements in biomedical research, developing sensitive and specific tools for recognizing biological motifs, such as cell receptors and proteins in complex biological solutions, remains a challenge. Furthermore, current approaches often rely on complex biological derivatives like antibodies, lacking a cost-effective delivery strategy. Our study proposes creating and characterizing a novel hybrid metal oxide polymer nanoparticle named IONPPP, functionalized with a DNA aptamer designed to recognize HER2-positive cells. HER2 is a clinically actionable marker for gastric, gastroesophageal, and, particularly, breast cancers. This unique combination of a metal core with an external polymeric structure offers the potential for identification, isolation, and even theragnostic applications, benefiting from its low toxicity and high specificity.

2.

Graphical Abstract
ATP binding cassette transporters and uridine diphosphate glycosyltransferases are ancient protein families that evolved roles in herbicide resistance through exaptation
Authors: Caygill Samuel , Dolan Liam
Published: June 2023

ATP-binding cassette (ABC) transporters actively transport various substances across membranes, while uridine diphosphate (UDP) glycosyltransferases (UGTs) are proteins that catalyse the chemical modification of various organic compounds. Both of these protein superfamilies have been associated with conferring herbicide resistance in weeds. Little is known about the evolutionary history of these protein families in the Archaeplastida. To infer the evolutionary histories of these protein superfamilies, we compared protein sequences collected from 10 species which represent distinct lineages of the Archaeplastida – the lineage including glaucophyte algae, rhodophyte algae, chlorophyte algae and the streptophytes – and generated phylogenetic trees. We show that ABC transporters were present in the last common ancestor of the Archaeplastida which lived 1.6 billion years ago, and the major clades identified in extant plants were already present then. Conversely, we only identified UGTs in members of the streptophyte lineage, which suggests a loss of these proteins in earlier diverging Archaeplastida lineages or arrival of UGTs into a common ancestor of the streptophyte lineage through horizontal gene transfer from a non-Archaeplastida eukaryote lineage. We found that within the streptophyte lineage, most diversification of the UGT protein family occurred in the vascular lineage, with 17 of the 20 clades identified in extant plants present only in vascular plants. Based on our findings, we conclude that ABC transporters and UGTs are ancient protein families which diversified during Archaeplastida evolution, which may have evolved to for developmental functions as plants began to occupy new environmental niches and are now being selected to confer resistance to a diverse range of herbicides in weeds.
Neurobehavioral effects of fungicides in zebrafish: a systematic review and meta-analysis
Authors: Reis Carlos G. , Bastos Leonardo M. , Chitolina Rafael , Gallas-Lopes Matheus , Zanona Querusche K. , Becker Sofia Z. , Herrmann Ana P. , Piato Angelo
Published: June 2023

With the aim of yielding high productivity levels, pesticides are widely used in global agriculture. Among them, fungicides are compounds intended to inhibit fungal proliferation in crops and seeds. Their application often leads to environmental contamination, with these chemicals persistently being detected in surface waters. This presence may threaten non-target organisms that dwell in the affected ecosystems, including humans. In toxicologic research, the zebrafish (Danio rerio) is the most used fish species to assess the potential effects of fungicide exposure, generating numerous and sometimes conflicting findings. We conducted a systematic review and meta-analysis aiming to synthesize the neurobehavioral effects of fungicides in zebrafish. The search was performed in three databases (PubMed, Scopus, and Web of Science) and the screening was based on a two-stage process guided by pre-defined inclusion/exclusion criteria. Qualitative and quantitative data, as well as reporting quality, were extracted from the included studies (n = 60). Meta-analyses were performed for the outcomes of distance traveled in larvae and adults, and spontaneous movements in embryos. We found an overall significant effect of fungicide exposure on distance, which was lower in exposed versus control groups (SMD −0.44 [−0.74; −0.13], p = 0.0055). No effect was observed for spontaneous movements. The overall heterogeneity for distance and spontaneous movements was considered high (I2= 80%) and moderate (I2= 74%), respectively. This can be explained by substantial methodological variation between protocols, whereas a poor reporting practice hinders the proper critical evaluation of the findings. However, a sensitivity analysis did not indicate any study skewing the meta-analyses. This review demonstrates the need for better-designed and reported experiments in this field.

Highlights

-

We systematically reviewed the behavioral effects of fungicides in zebrafish

-

Fungicides decrease the distance traveled

-

Fungicide exposure has no significant effects on spontaneous movements

-

Moderate to high levels of heterogeneity were found

-

The results showed a need for better-designed studies with clarity of report
The zinc transporter Slc30a1 in macrophages plays a protective role againstSalmonellainfection
Authors: Na-Phatthalung Pinanong , Sun Shumin , Xie Enjun , Wang Jia , Min Junxia , Wang Fudi
Published: June 2023

The zinc transporter Slc30a1 plays an essential role in maintaining cellular zinc homeostasis; however, its functional role in macrophages remains largely unknown. Here, we systematically examined the expression and function of Slc30a1 in macrophages uponSalmonellainfection in both Slc30a1 reporter mice and in macrophage-specificSlc30a1knockout (Slc30a1fl/flLysMCre) mice. We found thatSlc30a1fl/flLysMCremice have an increased susceptibility toSalmonellainfection compared to control littermates. Mechanistically, we found that loss of Slc30a1 in macrophages reduced their bactericidal activity via reduced iNOS and NO production due to intracellular zinc accumulation. In addition, we observed significantly increased expression ofMt1(metallothionein 1) inSalmonella-infectedSlc30a1-deficient macrophages, suggesting that Mt1 may serve as a compensatory zinc reservoir. Interestingly, macrophages lacking bothMt1andSlc30a1expression (Slc30a1fl/flLysMCre; Mt1-/-) had increased cell death uponSalmonellainfection due to excess zinc-induced oxidative stress. Taken together, our results show that Slc30a1 in macrophages can protect againstSalmonellainfection, providing mechanistic insights into the role of Slc30a1-mediated zinc homeostasis in macrophages in response to infectious disease.
Unpredictable soil conditions affect the prevalence of a microbial symbiosis
Authors: Scott Trey J. , Stephenson Calum J. , Rao Sandeep , Queller David C. , Strassmann Joan E.
Published: June 2023

The evolution of symbiotic interactions may be affected by unpredictable conditions. However, a link between prevalence of symbiosis and these conditions has not been widely demonstrated. We test for these associations usingDictyostelium discoideumsocial amoebae and their bacterial symbionts.D. discoideumare host to endosymbiotic bacteria from three taxa:Paraburkholderia, AmoebophilusandChlamydiae. Three species of facultativeParaburkholderiasymbionts are the best studied and give hosts the ability to carry food bacteria through the dispersal stage to new environments.AmoebophilusandChlamydiaeare obligate endosymbionts with no measurable impact on host fitness. We test whether the frequency of both single infections and coinfections of these symbionts are associated with the unpredictability of their soil environments by using symbiont presence-absence data from soil isolates from 21 locations across the eastern United States. We find that thatAmoebophilusandChlamydiaeobligate endosymbionts and coinfections are not associated with any of our mean measures, but that unpredictable precipitation can promote or hinder symbiosis depending on the species ofParaburkholderiasymbiont.
Accelerating Cancer Vaccine Development for Human T-Lymphotropic Virus (HTLV) Using a High-Throughput Molecular Dynamics Approach
Authors: Moin Abu Tayab , Rani Nurul Amin , Ullah Md. Asad , Patil Rajesh B. , Robin Tanjin Barketullah , Nawal Nafisa , Zubair Talha , Mahamud Syed Iftakhar , Sakib Mohammad Najmul , Islam Nafisa Nawal , Khaleque Md. Abdul , Absar Nurul , Shohael Abdullah Mohammad
Published: June 2023

Human T-lymphotropic virus (HTLV), a retrovirus belonging to the oncovirus family, has long been linked to be associated with various inflammatory and immunosuppressive disorders. To combat the devastating impact of this virus, our study employed a reverse vaccinology approach to design a multi-epitope-based vaccine targeting the highly virulent subtypes of HTLV. We conducted a comprehensive analysis of the molecular interactions between the vaccine and Toll-like receptors (TLRs), providing valuable insights for future research on preventing and managing HTLV-related diseases and any possible outbreaks. The vaccine was designed by focusing on the envelope glycoprotein gp62, a crucial protein involved in the infectious process and immune mechanisms of HTLV inside the human body. Epitope mapping identified T cell and B cell epitopes with low binding energies, ensuring their immunogenicity and safety. Linkers and adjuvants were incorporated to enhance the vaccine’s stability, antigenicity, and immunogenicity. Two vaccine constructs were developed, both exhibiting high antigenicity and conferring safety. Vaccine construct 2 demonstrated expected solubility and structural stability after disulfide engineering. Molecular docking analyses revealed strong binding affinity between the vaccine construct 2 and both TLR2 and TLR4. Molecular dynamics simulations indicated that the TLR2-vaccine complex displayed enhanced stability, compactness, and consistent hydrogen bond formation, suggesting a favorable affinity. Contact analysis, Gibbs free energy landscapes, and DCC analysis further supported the stability of the TLR2-vaccine complex, while DSSP analysis confirmed stable secondary structures. MM-PBSA analysis revealed a more favorable binding affinity of the TLR4-vaccine complex, primarily due to lower electrostatic energy. In conclusion, our study successfully designed a multi-epitope-based vaccine targeting HTLV subtypes and provided valuable insights into the molecular interactions between the vaccine and TLRs. These findings should contribute to the development of effective preventive and treatment approaches against HTLV-related diseases.
Oxidation of hemoproteins byStreptococcus pneumoniaecollapses the cell cytoskeleton and disrupts mitochondrial respiration leading to cytotoxicity of human lung cells
Authors: Scasny Anna , Alibayov Babek , Khan Faidad , Rao Shambavi J. , Murin Landon , Jop Vidal Ana G. , Smith Perriann , Wei Li , Edwards Kristin , Warncke Kurt , Vidal Jorge E.
Published: June 2023

Streptococcus pneumoniae(Spn) causes pneumonia that kills millions through acute toxicity and invasion of the lung parenchyma. During aerobic respiration, Spn releases hydrogen peroxide (Spn-H2O2), as a by-product of enzymes SpxB and LctO, and causes cell death with signs of both apoptosis and pyroptosis by oxidizing unknown cell targets. Hemoproteins are molecules essential for life and prone to oxidation by H2O2. We recently demonstrated that during infection-mimicking conditions, Spn-H2O2oxidizes the hemoprotein hemoglobin (Hb), releasing toxic heme. In this study, we investigated details of the molecular mechanism(s) by which the oxidation of hemoproteins by Spn-H2O2causes human lung cell death. Spn strains, but not H2O2-deficient SpnΔspxBΔlctOstrains caused time-dependent cell cytotoxicity characterized by the rearrangement of the actin, the loss of the microtubule cytoskeleton and nuclear contraction. Disruption of the cell cytoskeleton correlated with the presence of invasive pneumococci and an increase of intracellular reactive oxygen species. In cell culture, the oxidation of Hb or cytochrome c (Cytc) caused DNA degradation and mitochondrial dysfunction from inhibition of complex I-driven respiration, which was cytotoxic to human alveolar cells. Oxidation of hemoproteins resulted in the creation of a radical, which was identified as a protein derived side chain tyrosyl radical by using electron paramagnetic resonance (EPR). Thus, we demonstrate that Spn invades lung cells, releasing H2O2that oxidizes hemoproteins, including Cytc, catalyzing the formation of a tyrosyl side chain radical on Hb and causing mitochondrial disruption, that ultimately leads to the collapse of the cell cytoskeleton.
Anoctamin-1 is induced by TGF-beta and contributes to lung myofibroblast differentiation
Authors: Reed Eleanor B. , Orbeta Shaina , Miao Bernadette A. , Sitikov Albert , Chen Bohao , Levitan Irena , Solway Julian , Mutlu Gökhan M. , Fang Yun , Mongin Alexander A. , Dulin Nickolai O.
Published: June 2023

Idiopathic pulmonary fibrosis (IPF) is a devastating disease characterized by progressive scarring of the lungs and resulting in deterioration in lung function. Transforming growth factor-beta (TGF-β) is one of the most established drivers of fibrotic processes. TGF-β promotes transformation of tissue fibroblasts to myofibroblasts, a key finding in the pathogenesis of pulmonary fibrosis. We report here that TGF-β robustly upregulates the expression of the calcium-activated chloride channel Anoctamin-1 (ANO1) in human lung fibroblasts (HLF) at mRNA and protein levels. ANO1 is readily detected in fibrotic areas of IPF lungs in the same area with smooth muscle alpha-actin (SMA)-positive myofibroblasts. TGF-β-induced myofibroblast differentiation (determined by the expression of SMA, collagen-1 and fibronectin) is significantly inhibited by a specific ANO1 inhibitor, T16Ainh-A01, or by siRNA-mediated ANO1 knockdown. T16Ainh-A01 and ANO1 siRNA attenuate pro-fibrotic TGF-β signaling, including activation of RhoA pathway and AKT, without affecting initial Smad2 phosphorylation. Mechanistically, TGF-β treatment of HLF results in a significant increase in intracellular chloride levels, which is prevented by T16Ainh-A01 or by ANO1 knockdown. The downstream mechanism involves the chloride-sensing “with-no-lysine (K)” kinase (WNK1). WNK1 siRNA significantly attenuates TGF-β-induced myofibroblast differentiation and signaling (RhoA pathway and AKT), whereas the WNK1 kinase inhibitor WNK463 is largely ineffective. Together, these data demonstrate that (i) ANO1 is a TGF-β-inducible chloride channel that contributes to increased intracellular chloride concentration in response to TGF-β; and (ii) ANO1 mediates TGF-β-induced myofibroblast differentiation and fibrotic signaling in a manner dependent on WNK1 protein, but independent of WNK1 kinase activity.

NEW & NOTEWORTHY

This study describes a novel mechanism of differentiation of human lung fibroblasts (HLF) to myofibroblasts – the key process in the pathogenesis of pulmonary fibrosis. TGF-β drives the expression of calcium-activated chloride channel anoctmin-1 (ANO1) leading to an increase in intracellular levels of chloride. The latter recruits chloride-sensitive With-No-Lysine (K) kinase (WNK1) to activate pro-fibrotic RhoA and AKT signaling pathways, possibly through activation of mammalian target of rapamycin complex-2 (mTORC2), altogether promoting myofibroblast differentiation.
Identification and functional analysis of novel stress-resistance genes from metagenomes of extreme environments
Authors: Juarez Joshelin Huanca , Nascimento Silva Edson do , Silva Ninna Hirata , Silva-Rocha Rafael , Guazzaroni María-Eugenia
Published: June 2023

Currently, industrial bioproducts are less competitive than chemically produced goods due to the shortcomings of conventional microbial hosts. Metagenomic approaches from extreme environments can provide useful biological parts to improve bacterial robustness to process-specific parameters. Here, in order to build synthetic genetic circuits that increase bacterial resistance to diverse stress conditions, we mined novel stress tolerance genes from metagenomic databases using anin silicoapproach based on Hidden-Markov-Model profiles. For this purpose, we used metagenomic shotgun sequencing data from microbial communities of extreme environments to identify genes encoding chaperones and other proteins that confer resistance to stress conditions. We identified and characterized ten novel protein-encoding sequences related to the DNA-binding protein HU, the ATP-dependent protease ClpP, and the chaperone protein DnaJ. By expressing these genes inEscherichia coliunder several stress conditions (including high temperature, acidity, oxidative and osmotic stress, and UV radiation), we identified five genes conferring resistance to at least two stress conditions when expressed inE. coli. Moreover, one of the identified HU coding-genes which was retrieved from an acidic soil metagenome increasedE. colitolerance to four different stress conditions, implying its suitability for the construction of a synthetic circuit directed to expand broad bacterial resistance.