Single Compartments Research Articles

Microplastics in multi-environmental compartments: Research advances, media, and global management scenarios

During the past decades, microplastics (MPs) have become an emerging concern due to their persistence and potential environmental threat. MP pollution has become so drastic that it has been found in the human food chain, breast milk, polar regions, and even the Himalayan basin, lake, etc. Inflammation, pulmonary hypertension, vascular occlusions, increased coagulability and blood cell cytotoxicity, disruption of immune function, neurotoxicity, and neurodegenerative diseases can all be brought on by severe microplastic exposure. Although many MPs studies have been performed on single environmental compartments, MPs in multi-environmental compartments have yet to be explored fully. This review aims to summarize the muti-environmental media, detection tools, and global management scenarios of MPs. The study revealed that MPs could significantly alter C flow through the soil-plant system, the structure and metabolic status of the microbial community, soil pH value, biomass of plant shoots and roots, chlorophyll, leaf C and N contents, and root N contents. This review reveals that MPs may negatively affect many C-dependent soil functions. Different methods have been developed to detect the MPs from these various environmental sources, including microscopic observation, density separation, Raman, and FT-IR analysis. Several articles have focused on MPs in individual environmental sources with a developed evaluation technique. This review revealed the extensive impacts of MPs on soil-plant systems, microbial communities, and soil functions, especially on water, suggesting possible disturbances to vital ecological processes. Furthermore, the broad range of detection methods explored emphasizes the significance of reliable analytical techniques in precisely evaluating levels of MP contamination in various environmental media. This paper critically discusses MPs' sources, occurrences, and global management scenarios in all possible environmental media and ecological health impacts. Future research opportunities and required sustainable strategies have also been suggested from Bangladesh and international perspectives based on challenges faced due to MP's pollution.

Abstract 5828: The genomic architecture of ibrutinib resistance in CLL: Oligoclonal progression with variable anatomical distribution

Abstract Progressive disease (PD) in patients with chronic lymphocytic leukemia (CLL) on ibrutinib often presents with acquired mutations in BTK and/or PLCG2. Reported variant allele frequencies (VAF) are often low, leading some to question the role of these mutations. Further, several co-existing mutations are often identified. Here we investigated the clonal composition of PD on single cell level, across time, and different anatomic compartments. 84 CLL patients (52 treatment-naïve; 32 relapsed/refractory) with either a TP53 aberration or age ≥65 years received single-agent ibrutinib 420 mg once daily until PD or limiting side effects on a phase 2 study (NCT01500733). The median progression-free survival was 86.6 months. 39 (46.4%) patients progressed, 31 with CLL (PD-CLL), and 8 with Richter’s transformation. Median time to PD-CLL was 57.2 months. In PD-CLL patients, peripheral blood (PB) was sent for genotyping of known hotspot mutations in BTK/PLCG2 (Neogenomics). We then designed digital droplet PCR probes to test for BTK C481S/R/Y and PLCG2 R665W/L845/S707F mutations in samples collected at baseline, during response to ibrutinib and at PD in 29 patients. 26 (89.7%) patients had detectable BTK/PLCG2 mutations (VAF range 0.04 - 0.96). 12 (41%) patients carried multiple BTK/PLCG2 mutations. In 11 evaluable cases single-cell DNA sequencing (Mission Bio) showed individual mutations present in separate cells consistent with branching evolution. Having confirmed oligoclonality, we calculated the cumulative cell fraction (cCF) of BTK/PLCG2 mutations in the 29 PD-CLL patients. 16 (55%) patients had cCF >0.5 (range 0.59-0.96), 10 patients (35%) had cCF < 0.5 (range 0.04-0.43) and 3 patients (10%) had no detectable mutations. BTK/PLCG2 mutations were detected in samples collected at median 21.6 months (range 0 - 75) prior to PD. In 11 cases, we tested lymph node (LN) biopsies at PD. In 6 cases with cCF <0.5 in PB, 4 corresponding LN samples had higher cCF (0.01/0.92; 0/0.85; 0.06/0.69; 0.46/0.99 for PB/LN, respectively). In 5 cases, PB contained 2-6 distinct subclones with cCF >0.5, in 3 cases the corresponding LN harbored fewer subclones than PB (6/3; 3/2; 3/0 for PB/LN, respectively). To characterize the genomic background of PD-CLL, we performed whole-exome sequencing of longitudinal samples from 26 patients. In addition to BTK/PLCG2, the most frequently mutated genes were TP53, SF3B1, NOTCH1, and POT1. Furthermore, copy number variations (CNA), such as del17p, del13q, del14q, del3p, and del8p, were common. In summary, in our cohort BTK/PLCG2 mutations were identified in 89.7% of PD-CLL patients. These mutations arise in oligoclonal populations with variable distribution across anatomical sites. In rare patients without BTK/PLCG2 mutations, the co-evolution of putative driver mutations and multiple CNAs generated genomic complexity reminiscent of lymphoma transformation. Citation Format: Chingiz Underbayev, Jonathan Chen, Hailey M. Harris, Lauren T. Vaughn, Andy Itsara, Adrian Wiestner. The genomic architecture of ibrutinib resistance in CLL: Oligoclonal progression with variable anatomical distribution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5828.

HsdSA regulated extracellular vesicle-associated PLY to protect Streptococcus pneumoniae from macrophage killing via LAPosomes.

S. pneumoniae is a major human pathogen that undergoes a spontaneous and reversible phase variation that allows it to survive in different host environments. Interestingly, we found hsdSA , a gene that manipulated the phase variation, promoted the survival and replication of S. pneumoniae in macrophages by regulating EV production and EV-associated PLY. More importantly, here we provided the first evidence that higher EV-associated PLY (produced by D39) could form LAPosomes that were single membrane compartments containing S. pneumoniae, which are induced by integrin β1/NOX2/ROS pathway. At the same time, EV-associated PLY increased the permeability of lysosome membrane and induced an insufficient acidification to escape the host killing, and ultimately prolonged the survival of S. pneumoniae in macrophages. In contrast, lower EV-associated PLY (produced by D39ΔhsdSA ) activated ULK1 recruitment to form double-layered autophagosomes to eliminate bacteria.

STARGATE-X: a Python package for statistical analysis on the REACTOME network.

Many important aspects of biological knowledge at the molecular level can be represented by pathways. Through their analysis, we gain mechanistic insights and interpret lists of interesting genes from experiments (usually omics and functional genomic experiments). As a result, pathways play a central role in the development of bioinformatics methods and tools for computing predictions from known molecular-level mechanisms. Qualitative as well as quantitative knowledge about pathways can be effectively represented through biochemical networks linking the biochemical reactions and the compounds (e.g., proteins) occurring in the considered pathways. So, repositories providing biochemical networks for known pathways play a central role in bioinformatics and in systems biology. Here we focus on Reactome, a free, comprehensive, and widely used repository for biochemical networks and pathways. In this paper, we: (1) introduce a tool StARGate-X (STatistical Analysis of the Reactome multi-GrAph Through nEtworkX) to carry out an automated analysis of the connectivity properties of Reactome biochemical reaction network and of its biological hierarchy (i.e., cell compartments, namely, the closed parts within the cytosol, usually surrounded by a membrane); the code is freely available at https://github.com/marinoandrea/stargate-x; (2) show the effectiveness of our tool by providing an analysis of the Reactome network, in terms of centrality measures, with respect to in- and out-degree. As an example of usage of StARGate-X, we provide a detailed automated analysis of the Reactome network, in terms of centrality measures. We focus both on the subgraphs induced by single compartments and on the graph whose nodes are the strongly connected components. To the best of our knowledge, this is the first freely available tool that enables automatic analysis of the large biochemical network within Reactome through easy-to-use APIs (Application Programming Interfaces).

Location-specific pathology analysis of the monopodial pulmonary vasculature in a rabbit model of bronchopulmonary dysplasia-A pilot study.

The mammalian pulmonary vasculature consists of functionally and morphologically heterogeneous compartments. When comparing sets of lungs, for example, in disease models or therapeutic interventions, local changes may be masked by the overall heterogeneity of the organ structure. Therefore, alterations taking place only in a sub-compartment may not be detectable by global analysis. In the monopodial lung, the characterization of distinct vessel groups is difficult, due to the asymmetrical branching pattern. In this pilot study, a previously established method to classify segments of the monopodial pulmonary arterial tree into homogeneous groups was employed. To test its suitability for experimental settings, the method was applied to a hyperoxia (HYX, ≥95% oxygen) rabbit model of bronchopulmonary dysplasia and a normoxic control group (NOX, 21% oxygen). The method allowed the identification of morphological differences between the HYX and the NOX groups. Globally visible differences in lumen diameter were pinpointed to specific lung regions. Furthermore, local changes of wall dimension and cell layers in single compartments, that would not have been identifiable in an unfocused analysis of the whole dataset, were found. In conclusion, the described method achieves a higher precision in morphological studies of lung disease models, compared to a common, global analysis approach.

Adaptive closed-loop paradigm of electrophysiology for neuron models

The traditional electrophysiological experiments based on an open-loop paradigm are relatively complicated and limited when facing an individual neuron with uncertain nonlinear factors. Emerging neural technologies enable tremendous growth in experimental data leading to the curse of high-dimensional data, which obstructs the mechanism exploration of spiking activities in the neurons. In this work, we propose an adaptive closed-loop electrophysiology simulation experimental paradigm based on a Radial Basis Function neural network and a highly nonlinear unscented Kalman filter. On account of the complex nonlinear dynamic characteristics of the real neurons, the proposed simulation experimental paradigm could fit the unknown neuron models with different channel parameters and different structures (i.e. single or multiple compartments), and further compute the injected stimulus in time according to the arbitrary desired spiking activities of the neurons. However, the hidden electrophysiological states of the neurons are difficult to be measured directly. Thus, an extra Unscented Kalman filter modular is incorporated in the closed-loop electrophysiology experimental paradigm. The numerical results and theoretical analyses demonstrate that the proposed adaptive closed-loop electrophysiology simulation experimental paradigm achieves desired spiking activities arbitrarily and the hidden dynamics of the neurons are visualized by the unscented Kalman filter modular. The proposed adaptive closed-loop simulation experimental paradigm can avoid the inefficiency of data at increasingly greater scales and enhance the scalability of electrophysiological experiments, thus speeding up the discovery cycle on neuroscience.

Pituitary adenoma with cavernous sinus compartment penetration and intracranial extension: surgical anatomy, approach, and outcomes.

To understand the different characteristics and growth corridors of knosp grade 4 pituitary adenomas (Knosp4PA) with cavernous sinus (CS) compartments penetration and intracranial extension, aiming to improve the safety, effectiveness, and total resection rate of surgery. A case series of 120 Knosp4PA patients with 187 invaded compartments were retrospectively reviewed. A novel surgery-relevant grading system was proposed according to the CS penetrating features. The details of approach drafting, risk prediction, and complication avoidance were analyzed and integrated through illustrated cases. All enrolled tumor was Knosp4PA which was derived from Knosp subgrades 3A(62.5%) and 3B(37.5%). Based on the tumor growth pathway and its relevant features, five subclassifications of intracranial extension(n=98,81.7%) were classified, which derived from the superior (Dolenc's and Oculomotor subtype, 5% and 24.2%), lateral (Parkinson's subtype,18.3%), and posterior (cerebral peduncle and Dorello's subtype, 5.8% and 1.7%) CS compartment penetration. The size of intracranial extension is assessed by Lou's scale proposed here based on preoperative MRI characteristics. Under Lou's scale, the gross total rate (GTR) decreased (82%, 53%, 22%, and 19%) with grades increased (grade 0,1,2,3, respectively), and presents significant difference between the four groups (p=0.000), as well as between single and multiple compartments involved (p=0.001). Preoperative cranial nerve deficits included the optic nerve (53%), oculomotor nerve (24.2%), and abducent nerve (4.2%), with an overall rate of visual function improvement in 68.1%. Postoperative complications of transient diabetes insipidus, cerebrospinal fluid (CSF) leakage, and cranial nerve deficits were 6.7%, 0.8%, and 0%. No new cranial nerve deficits occurred. The mortality rate was 0.8%. The concept of "penetration" refines the extracavernous growth pattern, and the five intracranial subclassifications help to understand the potential extension corridors, enhancing adequate exposure and targeted resection of Knosp4PA. This grading system may benefit from its predictive and prognostic value, from which a higher GTR rate can be achieved.

Quantification of Giant Unilamellar Vesicle Fusion Products by High-Throughput Image Analysis.

Artificial cells are based on dynamic compartmentalized systems. Thus, remodeling of membrane-bound systems, such as giant unilamellar vesicles, is finding applications beyond biological studies, to engineer cell-mimicking structures. Giant unilamellar vesicle fusion is rapidly becoming an essential experimental step as artificial cells gain prominence in synthetic biology. Several techniques have been developed to accomplish this step, with varying efficiency and selectivity. To date, characterization of vesicle fusion has relied on small samples of giant vesicles, examined either manually or by fluorometric assays on suspensions of small and large unilamellar vesicles. Automation of the detection and characterization of fusion products is now necessary for the screening and optimization of these fusion protocols. To this end, we implemented a fusion assay based on fluorophore colocalization on the membranes and in the lumen of vesicles. Fluorescence colocalization was evaluated within single compartments by image segmentation with minimal user input, allowing the application of the technique to high-throughput screenings. After detection, statistical information on vesicle fluorescence and morphological properties can be summarized and visualized, assessing lipid and content transfer for each object by the correlation coefficient of different fluorescence channels. Using this tool, we report and characterize the unexpected fusogenic activity of sodium chloride on phosphatidylcholine giant vesicles. Lipid transfer in most of the vesicles could be detected after 20 h of incubation, while content exchange only occurred with additional stimuli in around 8% of vesicles.

Optical and Electrochemical Probes for Monitoring Cytochrome c in Subcellular Compartments During Apoptosis.

Cytochrome c (Cyt. c) is a key initiator of the caspases that activate cell apoptosis. The spatiotemporal evaluation of the contents of Cyt. c in cellular compartments and the detection of Cyt. c delivery between cellular compartments upon apoptosis is important for probing cell viabilities. We introduce an optical probe and an electrochemical probe for the quantitative assessment of Cyt. c in cellular compartments at the single cell level. The optical or electrochemical probes are functionalized with photoresponsive o-nitrobenzylphosphate ester-caged Cyt. c aptamer constituents. These are uncaged by light stimuli at single cell compartments, allowing the spatiotemporal detection of Cyt. c through the formation of Cyt. c/aptamer complexes at non-apoptotic or apoptotic conditions. The probes are applied to distinguish the contents of Cyt. c in cellular compartments of epithelial MCF-10A breast cells and malignant MCF-7 and MDA-MB-231 breast cells under apoptotic/non-apoptotic conditions.

Optical and Electrochemical Probes for Monitoring Cytochrome c in Subcellular Compartments During Apoptosis

AbstractCytochrome c (Cyt. c) is a key initiator of the caspases that activate cell apoptosis. The spatiotemporal evaluation of the contents of Cyt. c in cellular compartments and the detection of Cyt. c delivery between cellular compartments upon apoptosis is important for probing cell viabilities. We introduce an optical probe and an electrochemical probe for the quantitative assessment of Cyt. c in cellular compartments at the single cell level. The optical or electrochemical probes are functionalized with photoresponsive o‐nitrobenzylphosphate ester‐caged Cyt. c aptamer constituents. These are uncaged by light stimuli at single cell compartments, allowing the spatiotemporal detection of Cyt. c through the formation of Cyt. c/aptamer complexes at non‐apoptotic or apoptotic conditions. The probes are applied to distinguish the contents of Cyt. c in cellular compartments of epithelial MCF‐10A breast cells and malignant MCF‐7 and MDA‐MB‐231 breast cells under apoptotic/non‐apoptotic conditions.

Environment Symmetry Drives a Multidirectional Code in Rat Retrosplenial Cortex.

We investigated how environment symmetry shapes the neural processing of direction by recording directionally tuned retrosplenial neurons in male Lister hooded rats exploring multicompartment environments that had different levels of global rotational symmetry. Our hypothesis built on prior observations of twofold symmetry in the directional tuning curves of rats in a globally twofold-symmetric environment. To test whether environment symmetry was the relevant factor shaping the directional responses, here we deployed the same apparatus (two connected rectangular boxes) plus one with fourfold symmetry (a 2 × 2 array of connected square boxes) and one with onefold symmetry (a circular open-field arena). Consistent with our hypothesis we found many neurons with tuning curve symmetries that mirrored these environment symmetries, having twofold, fourfold, or onefold symmetric tuning, respectively. Some cells expressed this pattern only globally (across the whole environment), maintaining singular tuning curves in each subcompartment. However, others also expressed it locally within each subcompartment. Because multidirectionality has not been reported in naive rats in single environmental compartments, this suggests an experience-dependent effect of global environment symmetry on local firing symmetry. An intermingled population of directional neurons were classic head direction cells with globally referenced directional tuning. These cells were electrophysiologically distinct, with narrower tuning curves and a burstier firing pattern. Thus, retrosplenial directional neurons can simultaneously encode overall head direction and local head direction (relative to compartment layout). Furthermore, they can learn about global environment symmetry and express this locally. This may be important for the encoding of environment structure beyond immediate perceptual reach.SIGNIFICANCE STATEMENT We investigated how environment symmetry shapes the neural code for space by recording directionally tuned neurons from the retrosplenial cortex of rats exploring single- or multicompartment environments having onefold, twofold, or fourfold rotational symmetry. We found that many cells expressed a symmetry in their head direction tuning curves that matched the corresponding global environment symmetry, indicating plasticity of their directional tuning. They were also electrophysiologically distinct from canonical head directional cells. Notably, following exploration of the global space, many multidirectionally tuned neurons encoded global environment symmetry, even in local subcompartments. Our results suggest that multidirectional head direction codes contribute to the cognitive mapping of the complex structure of multicompartmented spaces.

Studi Populasi dan Karakteristik Pohon Bertengger Celepuk Rinjani (Otus jolandae) di Beberapa Jalur Hutan Kemasyarakatan (HKM) Wanalestari Desa Karang Sidemen Kabupaten Lombok Tengah

Rinjani Scops Owl (Otus Jolandae) is an endemic fauna that is included in the family of owls that are found in several forests that have been in the boundary or in the ecosystem of Mount Rinjani. The latest report published by IUCN in 2016 on the Rinjani Scops Owl (Otus Jolandae) is included in the Near Threatened (almost threatened) category. The purpose of this research is to know the population and characteristics of the trees perched Rinjani Scops Owl (Otus Jolandae) in several public forest lines Wanalestari Karang Sidemen village, Central Lombok. The method used in this research is divided into preliminary studies and primary research, where preliminary studies have been a method of literary studies, interviews, and observations. Then the main research has the IPA (Index Point Of Ambudance) method, measurement Of environmental physical condition, and vegetation structure with single compartments. Analysis of the user data is quantitative and qualitative. Results showed that the total population of Rinjani Scops Owl (Otus Jolandae) across the observation line in Hkm Wanalestari amounted to 16 individuals with an density of population each between 0,76-1,27 ha. The tree of the perched Rinjani Scops Owl (Otus Jolandae) consists of six types, namely the Dadap (Erythrina variegata) tree, Jackfruit (Artocarpus Heterophyllius), Durian (Durio zibethinus), Pecan (Aleurites moluccanus), Randu (Ceiba pentandra) and avocado (Parsea americana). The height of the Tengger tree ranges between 5-9 meters, diameter between 31,4-76,6 cm, and an area of heading 31,7-113,4 m2. The average temperature of Rinjani Scops Owl (Otus Jolandae) habitat of 25.4-25.6 °C humidity 76,4-76,6% and light intensity ranged from 0.9-4.68 Lux.
 Key Words : Rinjani Scops Owl, Animals, Population, Characteristics of perched trees

Optical-facilitated single-entity electrochemistry

Single-entity electrochemistry focusing on the study of transient electrochemical process at the confined interface, has become a promising field that addresses questions from multi-disciplines such as cellular biology, material chemistry, organic chemistry, etc . It offers the fruitful information hidden in bulk electrochemical measurements. As the optical techniques improve in spatial and temporal resolution, the combination of electrochemistry with optical microspectroscopy provides more comprehensive information of single-entity electrochemistry. Herein, we review recent progress made in optical–electrochemical measurements covering three aspects from the precise localization and temperature measurements of single compartments, to the in-situ tracking of dynamic behaviors of single nanoparticles in electrochemical process, and to the monitoring confinement-controlled electrochemistry at the single molecule/ion level. The review demonstrates how these optical methods are innovatively integrated with single-entity sensing. It also reveals how these optical–electrochemical combinations push single-entity electrochemistry forward.

118-OR: Fat Distribution Patterns Predict Type 2 Diabetes Risk and Provide Insights into Prediabetic Metabolism

Objective: Fat accumulation in liver, pancreas, skeletal muscle, and visceral bed relates to type 2 diabetes (T2D) . However, distribution of fat in these compartments is heterogenous and it is unclear if specific distribution patterns indicate high T2D risk. We therefore investigated fat distribution patterns and their link to future T2D. Methods: From 2168 individuals without diabetes undergoing computed tomography in Japan, this case-cohort study included 658 randomly selected individuals and 146 incident cases of T2D with a 6-year follow-up. Data-driven analysis (k-means) was applied to develop clusters based on fat content in liver, pancreas, muscle, and visceral bed. Hazard ratios (HRs) for association of clusters and incident T2D were estimated using weighted Cox regression. In 3 individuals without diabetes with magnetic resonance imaging and metabolic phenotyping in Germany, cluster validation with additional assessment of glycemic traits from OGTTs was conducted. Results: We identified four clusters of fat distribution: cluster 1 (Hepatic steatosis cluster) , cluster 2 (Pancreatic steatosis cluster) , cluster 3 (Myosteatosis dominant cluster) , cluster 4 (Steatopenic cluster) . Compared with Steatopenic cluster, the adjusted-HRs (95%CIs) for incident T2D were 4.02 (2.27-7.12) in Hepatic steatosis cluster, 3.38 (1.65-6.91) in Pancreatic steatosis cluster, and 1.95 (1.07-3.54) in Myosteatosis dominant cluster. The clusters were replicated in the German cohort with similar distribution of AUC-glucose to the diabetes hazard in the Japanese cohort. Insulin sensitivity and insulin secretion were different across clusters with the lowest insulin sensitivity and highest insulin secretion in Hepatic steatosis cluster. Conclusions: Extending evidence about fat accumulation in single compartments, we identified specific patterns of fat distribution with different T2D risk presumably due to differences in insulin sensitivity and insulin secretion. Disclosure H.Yamazaki: None. N.Stefan: Advisory Panel; Gilead Sciences, Inc., GlaxoSmithKline plc., Sanofi, Consultant; AstraZeneca, Intercept Pharmaceuticals, Inc., Novo Nordisk, Pfizer Inc., Speaker's Bureau; AstraZeneca, Boehringer Ingelheim International GmbH, Lilly Diabetes, Merck Sharp & Dohme Corp. A.Fritsche: Advisory Panel; Boehringer Ingelheim International GmbH, Novo Nordisk, Sanofi-Aventis Deutschland GmbH. A.L.Birkenfeld: None. R.Wagner: Advisory Panel; Akcea Therapeutics, Daiichi Sankyo, Sanofi-Aventis Deutschland GmbH, Speaker's Bureau; Lilly, Novo Nordisk, Sanofi-Aventis Deutschland GmbH. M.Heni: Advisory Panel; Boehringer Ingelheim International GmbH, Research Support; Boehringer Ingelheim International GmbH, Sanofi, Speaker's Bureau; Amryt Pharma Plc, Boehringer Ingelheim International GmbH, Novo Nordisk. S.Tauchi: None. J.Machann: None. T.Haueise: None. Y.Yamamoto: None. M.Dohke: None. N.Hanawa: None. Y.Kodama: Other Relationship; Eisai Co., Ltd. A.Katanuma: None. Funding the German Center for Diabetes Research (DZD, 01GI0925) , the state of Baden-Württemberg (32-5400/58/2, Forum Gesundheitsstandort Baden-Württemberg) , and JSPS KAKENHI Grant Number 19K16978

Whole-Brain Network Models: From Physics to Bedside

Computational neuroscience has come a long way from its humble origins in the pioneering work of Hodgkin and Huxley. Contemporary computational models of the brain span multiple spatiotemporal scales, from single neuronal compartments to models of social cognition. Each spatial scale comes with its own unique set of promises and challenges. Here, we review models of large-scale neural communication facilitated by white matter tracts, also known as whole-brain models (WBMs). Whole-brain approaches employ inputs from neuroimaging data and insights from graph theory and non-linear systems theory to model brain-wide dynamics. Over the years, WBM models have shown promise in providing predictive insights into various facets of neuropathologies such as Alzheimer's disease, Schizophrenia, Epilepsy, Traumatic brain injury, while also offering mechanistic insights into large-scale cortical communication. First, we briefly trace the history of WBMs, leading up to the state-of-the-art. We discuss various methodological considerations for implementing a whole-brain modeling pipeline, such as choice of node dynamics, model fitting and appropriate parcellations. We then demonstrate the applicability of WBMs toward understanding various neuropathologies. We conclude by discussing ways of augmenting the biological and clinical validity of whole-brain models.

Enterococcus faecalis alters endo-lysosomal trafficking to replicate and persist within mammalian cells.

Enterococcus faecalis is a frequent opportunistic pathogen of wounds, whose infections are associated with biofilm formation, persistence, and recalcitrance toward treatment. We have previously shown that E. faecalis wound infection persists for at least 7 days. Here we report that viable E. faecalis are present within both immune and non-immune cells at the wound site up to 5 days after infection, raising the prospect that intracellular persistence contributes to chronic E. faecalis infection. Using in vitro keratinocyte and macrophage infection models, we show that E. faecalis becomes internalized and a subpopulation of bacteria can survive and replicate intracellularly. E. faecalis are internalized into keratinocytes primarily via macropinocytosis into single membrane-bound compartments and can persist in late endosomes up to 24 h after infection in the absence of colocalization with the lysosomal protease Cathepsin D or apparent fusion with the lysosome, suggesting that E. faecalis blocks endosomal maturation. Indeed, intracellular E. faecalis infection results in heterotypic intracellular trafficking with partial or absent labelling of E. faecalis-containing compartments with Rab5 and Rab7, small GTPases required for the endosome-lysosome trafficking. In addition, E. faecalis infection results in marked reduction of Rab5 and Rab7 protein levels which may also contribute to attenuated Rab incorporation into E. faecalis-containing compartments. Finally, we demonstrate that intracellular E. faecalis derived from infected keratinocytes are significantly more efficient in reinfecting new keratinocytes. Together, these data suggest that intracellular proliferation of E. faecalis may contribute to its persistence in the face of a robust immune response, providing a primed reservoir of bacteria for subsequent reinfection.

Roadmap for Long-Term Macroplastic Monitoring in Rivers

Macroplastic pollution in and around rivers negatively impacts human livelihood, and aquatic ecosystems. Monitoring data are crucial for better understanding and quantifying this problem, and for the design of effective intervention strategies. However, current monitoring efforts are often of short duration, or study single river compartments. We present a “Roadmap” to overcome the challenges related to the design and implementation of long-term riverine macroplastic monitoring strategies. This “Roadmap” can help accelerating the process of achieving structural monitoring through providing a stepwise approach, which links monitoring goals and research questions to the data and methods required to answer them. We identify four monitoring goals: 1) policy, 2) knowledge development, 3) operations, and 4) solutions. Linked to these, we provide a non-exhaustive list of 12 globally common research questions that are important to answer to reach these goals. The “Roadmap” takes these questions and links them to development levels of monitoring methods for each river compartment: 1) method development, 2) baseline assessment, and 3) long-term monitoring. At each level, specific questions can only be answered if the level is achieved for specific river compartments. For questions at higher levels, the previous levels need to be achieved first. This creates a clear stepwise approach to solve open challenges. With the “Roadmap”, we provide a new tool to support decision-making and planning of specific projects by policy makers. The “Roadmap” is a clear and stepwise, yet flexible framework that allows to add and remove elements based on new insights, available resources, and other relevant changes.

Using a General Mathematical Model to Quantify the Fontan Paradox of Elevated Central Venous Pressure and Diminished Cardiac Output

A variety of serious complications often associated with Fontan procedure to palliate single ventricle physiology are related to elevated central venous pressure (CVP) and diminished cardiac output (CO). This “Fontan Paradox” is a fundamental challenge because some interventions benefit one of these variables at the cost of the other. Animal models employed to address the Fontan Paradox are limited, and the multiple mechanical properties affecting CVP and CO are difficult to measure, control, and scale to humans. Although complex mathematical models of the cardiovascular system have provided insights, the need to solve model equations numerically require that all parameter values are known a priori—results only apply to a subject characterized by a specific set of assumed parameter values. In contrast, it has been shown that the equations characterizing minimal closed-loop models can be solved algebraically, yielding algebraic formulas for hemodynamic variables in terms of mechanical properties of the heart and vasculature. Therefore, the purpose of the present work is to derive algebraic formulas for CVP and CO to address the Fontan Paradox. First, we utilized a modified minimal closed-loop model consisting of a single ventricle, arterial and venous vascular compartments, and systemic and pulmonary resistances. The end-diastolic pressure-volume relationship was linearized, and mean arterial pressure was assumed to be regulated by renal control of blood volume. Equations were solved algebraically for CVP, CO, and venous pressures. The resulting formulas for CVP and CO incorporate only five groups of parameters characterizing the 1) efficiency of heart-vascular interaction, 2) relative cardiac contractility, 3) relative pulmonary resistance, 4) theoretical stroke volume at zero ventricular pressure, and 5) theoretical CO at zero CVP. Of these, only mean arterial pressure (controlled by blood volume) and systemic resistance require a choice to be made of either rectifying CVP or CO. Furthermore, these general formulas indicate that altering blood volume or systemic resistance to treat low CO has a greater negative impact on CVP in subjects with diastolic dysfunction or high pulmonary resistance. The present work thus provides a novel tool for clinical investigators to explore the mechanical basis of the Fontan Paradox.

Single Cell-like Systems Reveal Active Unidirectional and Light-Controlled Transport by Nanomachineries.

Cellular life depends on transport and communication across membranes, which is emphasized by the fact that membrane proteins are prime drug targets. The cell-like environment of membrane proteins has gained increasing attention based on its important role in function and regulation. As a versatile scaffold for bottom-up synthetic biology and nanoscience, giant liposomes represent minimalistic models of living cells. Nevertheless, the incorporation of fragile multiprotein membrane complexes still remains a major challenge. Here, we report on an approach for the functional reconstitution of membrane assemblies exemplified by human and bacterial ATP-binding cassette (ABC) transporters. We reveal that these nanomachineries transport substrates unidirectionally against a steep concentration gradient. Active substrate transport can be spatiotemporally resolved in single cell-like compartments by light, enabling real-time tracking of substrate export and import in individual liposomes. This approach will help to construct delicate artificial cell-like systems.

Targeting GRK5 for Treating Chronic Degenerative Diseases.

G protein-coupled receptors (GPCRs) are the largest family of cell-surface receptors and they are responsible for the transduction of extracellular signals, regulating almost all aspects of mammalian physiology. These receptors are specifically regulated by a family of serine/threonine kinases, called GPCR kinases (GRKs). Given the biological role of GPCRs, it is not surprising that GRKs are also involved in several pathophysiological processes. Particular importance is emerging for GRK5, which is a multifunctional protein, expressed in different cell types, and it has been found located in single or multiple subcellular compartments. For instance, when anchored to the plasma membrane, GRK5 exerts its canonical function, regulating GPCRs. However, under certain conditions (e.g., pro-hypertrophic stimuli), GRK5 translocates to the nucleus of cells where it can interact with non-GPCR-related proteins as well as DNA itself to promote “non-canonical” signaling, including gene transcription. Importantly, due to these actions, several studies have demonstrated that GRK5 has a pivotal role in the pathogenesis of chronic-degenerative disorders. This is true in the cardiac cells, tumor cells, and neurons. For this reason, in this review article, we will inform the readers of the most recent evidence that supports the importance of targeting GRK5 to prevent the development or progression of cancer, cardiovascular, and neurological diseases.