Miracle-dz/UniFAR-FTUs huggingface dataset:
Proximity Dependent Biotinylation: Key Enzymes and Adaptation to Proteomics Approaches*

Proximity-dependent biotinylation approaches such as BioID and APEX overcome classical limitations of biochemical purification and have gained widespread use in recent years for revealing cellular neighborhoods. Here we focus on the structural diversity and mechanisms of the two classes of enzymes, biotin protein ligases and peroxidases, and discuss current and emerging applications of these enzymes for proximity dependent biotinylation. We provide guidelines for enzyme selection and experimental design for performing and interpreting proximity-dependent biotinylation experiments. Graphical Abstract Highlights Proximity-dependent biotinylation (PDB) approaches involve fusion of a bait with an enzyme. BioID (biotin protein ligase) and APEX (peroxidase) are distinct enzymes used in PDB. Past, present and future development and applications of PDB are discussed. We review labeling mechanisms and kinetics to provide guidance for experimental design. We discuss controls and considerations for data interpretation. The study of protein subcellular distribution, their assembly into complexes and the set of proteins with which they interact with is essential to our understanding of fundamental biological processes. Complementary to traditional assays, proximity-dependent biotinylation (PDB) approaches coupled with mass spectrometry (such as BioID or APEX) have emerged as powerful techniques to study proximal protein interactions and the subcellular proteome in the context of living cells and organisms. Since their introduction in 2012, PDB approaches have been used in an increasing number of studies and the enzymes themselves have been subjected to intensive optimization. How these enzymes have been optimized and considerations for their use in proteomics experiments are important questions. Here, we review the structural diversity and mechanisms of the two main classes of PDB enzymes: the biotin protein ligases (BioID) and the peroxidases (APEX). We describe the engineering of these enzymes for PDB and review emerging applications, including the development of PDB for coincidence detection (split-PDB). Lastly, we briefly review enzyme selection and experimental design guidelines and reflect on the labeling chemistries and their implication for data interpretation.
EF hand‐like motif mutations of Nav1.4 C‐terminus cause myotonic syndrome by impairing fast inactivation

Mutations of the voltage‐gated sodium channel gene (SCN4A), which encodes Nav1.4, cause nondystrophic myotonia that occasionally is associated with severe apnea and laryngospasm. There are case reports of nondystrophic myotonia due to mutations in the C‐terminal tail (CTerm) of Nav1.4, but the functional analysis is scarce.
Quantifying the socio-economic impact of leg lymphoedema on patient caregivers in a lymphatic filariasis and podoconiosis co-endemic district of Ethiopia

Background Lymphoedema caused by lymphatic filariasis (LF) or podoconiosis can result in physical disability and social exclusion, which is exacerbated by painful acute dermatolymphangioadenitis (ADLA) episodes. These conditions have a significant impact on patients, however, little is known about the indirect effects on their caregivers. This study, therefore, aimed to determine the impact on caregivers for patients with leg lymphoedema in a co-endemic district of Ethiopia. Methodology/Principal findings A cross-sectional survey of lymphoedema patients and their caregivers was conducted using semi-structured questionnaires in the Southern Nation Nationalities Peoples Region (SNNPR) of Ethiopia. Lymphoedema patient information on clinical severity (mild, moderate, severe), frequency of ADLAs, their socio-demographic characteristics and the identity of main caregiver(s) was collected. Caregiver information on socio-demographic characteristics, types of care provided, their quality of life (QoL) measured across nine domains, and productivity was collected, with key indicators compared in the presence and absence of patients’ ADLAs. A total of 73 patients and 76 caregivers were included. Patients were grouped by mild/moderate (n = 42, 57.5%) or severe (n = 31, 42.5%) lymphoedema, and reported an average of 6.1 (CI± 2.18) and 9.8 (CI± 3.17) ADLAs respectively in the last six months. A total of 48 (65.8%) female and 25 (34.2%) male patients were interviewed. Caregivers were predominately male (n = 45, 59.2%), and spouses formed the largest caregiving group for both female and male patients. In the absence of an ADLA, most caregivers (n = 42, 55.2%) did not provide care, but only one caregiver did not provide care during an ADLA. In the absence of an ADLA, the average time (hour:minute) spent by mild/moderate (00:17, CI: ± 00:08) and severe (00:10, CI: ± 00:07) patient caregiver per task was minimal. The time mild/moderate (00:47, CI: ± 00:11) and severe (00:51, CI: ± 00:16) patient caregivers spent per task significantly increased in the presence of an ADLA. In addition, caregivers’ QoL was negatively impacted when patients experienced an ALDA, and they had to forfeit an average of 6 to 7 work/school days per month. Conclusion/Significance Lymphoedema and ADLAs impact negatively on patients’ and their caregivers’ lives. This emphasises the importance of increasing access to effective morbidity management and disability prevention services to reduce the burden and help to address the Sustainable Development Goal (SDG) 5, target 5.4, which seeks to recognise and value unpaid care and domestic work.
Red herrings in crossmatching kidneys for transplant

Crossmatching of prospective renal transplant donors against recipients is a mandatory component of the transplant workup, being performed for over 40 years now. Allografting patients with human leukocyte antigens which are recognized by preformed antibodies constitutes the main cause of hyperacute or acute rejections. The existence of these donor-specific anti-human leukocyte antigen antibodies (DSAs) is regarded as a contraindication for graft trans-plantation, both cadaveric and live kidney. We present two unusual cases in which both complement-dependent cytotoxicity crossmatch and DSA by Luminex were falsely positive due to autoimmune and infectious causes, but single-antigen bead assay showed these antibodies to be against nondonor antigens. After treating their basic disease, thought to be responsible for false-positive DSA, these patients became DSA negative and underwent transplantation with an uneventful posttransplant period. Our aim through these examples is to highlight the problem of false-positive crossmatch in potential renal allograft transplant recipients. Further, we propose antigenic determination of donor-specific antibodies in such patients where we suspect the immune system to be chronically activated to pick up false-positive cases and therefore increase the donor pool without compromising the transplant outcome.
Anterolateral hip pain: Sonographic evaluation of the proximal iliotibial band and tensor fascia lata

Anterolateral hip pain is a common condition with variable etiologies that are associated with either the joint itself or the surrounding soft tissues. Abnormalities at the origin of the iliotibial band (ITB) and tensor fascia lata (TFL) including tendinosis and tears are increasingly appreciated as sources of pain and tenderness at the anterolateral aspect of the hip, specifically at the iliac crest. The exact cause for proximal ITB abnormality has not been delineated, but is likely a result of repetitive microtrauma or chronic mechanical stress (ie, among runners and endurance athletes). Determining the exact etiology of anterolateral hip pain is important because of the implications for treatment. An accurate diagnosis requires both a thorough physical examination and appropriate choice of imaging modality. Literature regarding imaging of the ITB/TFL origin has previously focused on MRI as the primary diagnostic imaging method. However, there are an increasing number of circumstances for which ultrasonography (US) has proven superior to MRI: (a) the evaluation for tenderness can be correlated with an anatomic structure during the US examination; (b) the affected side can be compared to the asymptomatic side; (c) USguided diagnostic and therapeutic procedures can be performed at the time of the examination if needed. In this pictorial essay, which highlights the US appearance of the normal proximal ITB/TFL origin and common abnormalities affecting this structure, a Philips iU22 scanner with a 12.5-MHz linear transducer (Philips Healthcare, Bothell, WA) was used.
News Feature: The best strategy for using trees to improve climate and ecosystems? Go natural

Despite big headlines and big money devoted to massive tree-planting projects that pledge to stave off desertification, the most effective method may be nurturing native seeds, rootstocks, and trees. Near the start of the rainy season in June 1983, Tony Rinaudo hauled a load of trees in his truck to be planted in remote villages in the Maradi region of Niger. Driving onto sandy soil, Rinaudo stopped to let air out of his tires to get better traction, and was hit by a sense of futility. For years, the Australian missionary had been working to improve the lives of people in one of the poorest countries in Africa by planting trees. But it wasn’t working. Most of the trees died or were pulled out by farmers. Standing beside his truck, all he could see was dusty barren plain, broken by a few scraggly bushes. “It dawned on me that I was wasting my time,” he says. Starting in 1985, 20 years of regeneration transformed barren, degraded land in the African Burkina Faso village of Ranawa into a fertile farm. Image credit: Chris Reij (World Resources Institute, Washington, DC). A man of deep faith, Rinaudo asked God for guidance. In a moment of clarity, his eye caught sight of one of the bushes. At closer look, he realized that it was no mere bush or weed; instead, it was a potentially valuable native tree—if permitted to grow. There was no need to plant trees; they were already there. “At that moment everything changed,” he says. Even a seeming desert harbors tree stumps, roots, and seeds that can be encouraged and nurtured—“a treasure chest waiting to be released,” says Rinaudo. “And if you allow some trees to grow, amazing things happen. ” Rinaudo’s epiphany led local farmers to add at least 200 million …
The role of xenobiotic-metabolizing enzymes in the placenta: a growing research field

ABSTRACT Introduction: The placenta is a temporary and unique organ that allows for the physical connection between a mother and fetus; this organ regulates the transport of gases and nutrients mediating the elimination of waste products contained in the fetal circulation. The placenta performs metabolic and excretion functions, on the basis of multiple enzymatic systems responsible for the oxidation, reduction, hydrolysis, and conjugation of xenobiotics. These mechanisms give the placenta a protective role that limits the fetal exposure to harmful compounds. During pregnancy, some diseases require uninterrupted treatment even if it is detrimental to the fetus. Drugs and other xenobiotics alter gene expression in the placenta with repercussions for the fetus and mother’s well-being. Areas covered: This review provides a brief description of the human placental structure and function, the main drug and xenobiotic transporters and metabolizing enzymes, placenta-metabolized substrates, and alterations in gene expression that the exposure to xenobiotics may cause. Expert opinion: Research should be focused on the identification and validation of biological markers for the assessment of the harmful effects of some drugs in pregnancy, including the evaluation of polymorphisms and methylation patterns in chorionic villous samples and/or amniotic fluid.
Bladder-sparing treatment options in localized muscle-invasive bladder cancer

ABSTRACT Introduction: Bladder cancer is the 9th most common cancer in the world and the 4th and 8th most common cancer diagnosed in men in the United States and United Kingdom respectively. The standard of care for the treatment of MIBC is radical cystectomy. Bladder preserving treatment approaches are emerging for select patients and should be considered strongly in patients who decline a radical cystectomy. Areas covered: In this review we look at the European and American recommended guidelines, the current standard of care, bladder-preserving options in MIBC, trimodal therapy and discuss future developments in the identification of molecular biomarkers that can predict therapeutic outcomes. Expert opinion: We strongly advocate bladder preservation for the right patient with strict criteria for enrolling patients in bladder preservation. The development of a specialized bladder cancer clinic could facilitate the selection of patients to be offered trimodal therapy. We believe that the future of bladder cancer will involve individualized care plans based upon clinical, radiological, endoscopic and molecular assessments.
Importance of Spatial Resolution in Global Groundwater Modeling

Global‐scale gradient‐based groundwater models are a new endeavor for hydrologists who wish to improve global hydrological models (GHMs). In particular, the integration of such groundwater models into GHMs improves the simulation of water flows between surface water and groundwater and of capillary rise and thus evapotranspiration. Currently, these models are not able to simulate water table depth adequately over the entire globe. Unsatisfactory model performance compared to well observations suggests that a higher spatial resolution is required to better represent the high spatial variability of land surface and groundwater elevations. In this study, we use New Zealand as a testbed and analyze the impacts of spatial resolution on the results of global groundwater models. Steady‐state hydraulic heads simulated by two versions of the global groundwater model G3M, at spatial resolutions of 5 arc‐minutes (9 km) and 30 arc‐seconds (900 m), are compared with observations from the Canterbury region. The output of three other groundwater models with different spatial resolutions is analyzed as well. Considering the spatial distribution of residuals, general patterns of unsatisfactory model performance remain at the higher resolutions, suggesting that an increase in model resolution alone does not fix problems such as the systematic overestimation of hydraulic head. We conclude that (1) a new understanding of how low‐resolution global groundwater models can be evaluated is required, and (2) merely increasing the spatial resolution of global‐scale groundwater models will not improve the simulation of the global freshwater system.
Elevation of intracranial pressure affects the relationship between hemoglobin concentration and neuronal activation in human somatosensory cortex

During neuronal activation, a local decrease of deoxygenated hemoglobin concentration (deoxy‐Hb) occurs which is the basis of functional brain imaging with blood oxygenation level dependent functional magnetic resonance imaging (BOLD‐fMRI). Elevated intracranial pressure (eICP) has been shown to impair functional deoxy‐Hb changes. This study investigated this effect and its relation to the underlying neuronal activity in the human primary somatosensory cortex (SI). Functional near‐infrared spectroscopy (fNIRS) during somatosensory evoked potentials (SEP) monitoring was performed on 75 subjects during conditions of median nerve stimulation (MNS) and resting state, combined with normal breathing (NB) and eICP by escalating breathing maneuvers (breath holding [BH], Valsalva maneuver with 15 mmHg [V15] and 35 mmHg expiratory pressure [V35]). During NB, fNIRS revealed a typical oxygenated hemoglobin concentration (oxy‐Hb) increase with deoxy‐Hb decrease during MNS enabling SI brain mapping. Breathing maneuvers associated eICP produced a known global change of oxy‐Hb and deoxy‐Hb with and without MNS. When subtracting measurements during resting state from measurements during MNS, neither functional oxy‐Hb nor deoxy‐Hb changes could be recovered while SEPs remained unchanged. In conclusion, Valsalva‐induced eICP prevents oxy‐Hb and deoxy‐Hb changes during neuronal activation in SI. This finding raises questions on the validity of oxy‐Hb‐ and deoxy‐Hb‐based brain imaging (e.g., BOLD‐fMRI) during eICP.
Extracellular Matrix Production by Mesenchymal Stromal Cells in Hydrogels Facilitates Cell Spreading and Is Inhibited by FGF‐2

In native tissues, the interaction between cells and the surrounding extracellular matrix (ECM) is reciprocal, as cells not only receive signals from the ECM but also actively remodel it through secretion of cell‐derived ECM. However, very little is known about the reciprocal interaction between cells and their secreted ECM within synthetic biomaterials that mimic the ECM for use in engineering of tissues for regenerative medicine or as tissue models. Here, poly(ethylene glycol) (PEG) hydrogels with fully defined biomaterial properties are used to investigate the emerging role of cell‐derived ECM on culture outcomes. It is shown that human mesenchymal stromal cells (MSCs) secrete ECM proteins into the pericellular space early after encapsulation and that, even in the absence of material‐presented cell adhesion motifs, cell‐derived fibronectin enables cell spreading. Then, it is investigated how different culture conditions influence MSC ECM expression in hydrogels. Most strikingly, it is found by RNA sequencing that the fibroblast growth factor 2 (FGF‐2) changes ECM gene expression and, in particular, decreases the expression of structural ECM components including fibrillar collagens. In summary, this work shows that cell‐derived ECM is a guiding cue in 3D hydrogels and that FGF‐2 is a potentially important ECM regulator within bioengineered cell and tissue systems.
Outpatient treatment for adults with complex eating disorders and co-morbid conditions: a decision making model and case example

ABSTRACT Although Cognitive Behavioral Therapy (CBT-E) for eating disorders has the most empirical support for the outpatient treatment of adult eating disorders (EDs), this model does not include a focus on intense emotion dysregulation, suicidality, and non-suicidal self-injury (NSSI). Furthermore, a subset of patients do not achieve sustained remission with CBT-E. Given that Dialectical Behavior Therapy (DBT) was designed for treatment refractory, complex patients, clinicians must be able to use assessment information to determine which type of treatment to use. The aims of this manuscript are to 1) describe a DBT-based and research-informed conceptual model for treatment decision making for an outpatient non-academic setting, 2) present a case example of a client with significant ED symptoms and complex medical and psychiatric comorbidities, using this decision making model and 3) present descriptive data from a private practice setting in which patients are referred to DBT vs. CBT-E according to this decision making model.
GeC/GaN vdW Heterojunctions: a Promising Photocatalyst for Overall Water Splitting and Solar Energy Conversion.

Two-dimensional van der Waals (vdW) heterojunctions have been regarded as promising candidates for photocatalytic water splitting and solar energy conversion. Here, we propose a two-dimensional GeC/GaN vdW heterostructure, where GaN monolayer and GeC monolayer are stacked. The binding energy, phonon spectrum, and elastic constants demonstrate this ma- terial's high dynamic and mechanical stability. Most notably, GW band structure, GW+BSE optical absorption spectrum, and band alignment of DFT scheme and empirical formula reveal that the GeC/GaN vdW heterostructures have a dramatically high optical absorption coeffi- cients (∼ 105 cm-1) in the visible region, a suitable band edge with sufficiently large kinetic over-potentials of the hydrogen evolution reaction (ΔEc ≥ 1:945 eV) and the oxygen evolu- tion reaction (ΔEv ≥ 1:244 eV). Photogenerated electrons and holes aggregate on the GeC monolayer and GaN monolayer surfaces, respectively, which could make this heterojunction a promising candidate for photocatalytic water splitting and solar energy conversion.
Structure specific recognition of telomeric repeats containing RNA by the RGG-box of hnRNPA1

Abstract The telomere repeats containing RNA (TERRA) is transcribed from the C-rich strand of telomere DNA and comprises of UUAGGG nucleotides repeats in humans. The TERRA RNA repeats can exist in single stranded, RNA-DNA hybrid and G-quadruplex forms in the cell. Interaction of TERRA RNA with hnRNPA1 has been proposed to play critical roles in maintenance of telomere DNA. hnRNPA1 contains an N-terminal UP1 domain followed by an RGG-box containing C-terminal region. RGG-motifs are emerging as key protein motifs that recognize the higher order nucleic acid structures as well as are known to promote liquid-liquid phase separation of proteins. In this study, we have shown that the RGG-box of hnRNPA1 specifically recognizes the TERRA RNA G-quadruplexes that have loops in their topology, whereas it does not interact with the single-stranded RNA. Our results show that the N-terminal UP1 domain in the presence of the RGG-box destabilizes the loop containing TERRA RNA G-quadruplex efficiently compared to the RNA G-quadruplex that lacks loops, suggesting that unfolding of G-quadruplex structures by UP1 is structure dependent. Furthermore, we have compared the telomere DNA and TERRA RNA G-quadruplex binding by the RGG-box of hnRNPA1 and discussed its implications in telomere DNA maintenance.
The Importance of Context in Moral Judgments

There is a gap between morality as experienced and morality as studied. In our personal and professional lives, moral judgments are embedded within a specific context. We know the who, what, where, and when and often can infer the why; we know the broader context of actions; and we may have a specific relationship with the actors. However, scholarly theorizing is often built on inferences from participants’ responses to decontextualized, impoverished stimuli. In our quest for uncovering general psychological truths, moral psychologists have examined evaluations of poorly guarded trolleys, strangers with odd sexual proclivities, and endorsement of abstract principles. The four articles included in this section demonstrate the power of contextualizing morality. In the current article, I place these papers within a broader framework for how scholars can contextualize morality research. I then argue why contextualizing morality matters: not only do contextualized questions better reflect the nuances of reality but also contextualized judgments might be key for improving predictions of moral behavior and understanding moral change.
Genetically encoded stealth nanoparticles of a zwitterionic polypeptide-paclitaxel conjugate have a wider therapeutic window than Abraxane in multiple tumor models.

Small-molecule therapeutics demonstrate sub-optimal pharmacokinetics and bioavailability due to their hydrophobicity and size. One way to overcome these limitations-and improve their efficacy-is to use "stealth" macromolecular carriers that evade uptake by the reticuloendothelial system. Although unstructured polypeptides are of increasing interest as macromolecular drug carriers, current recombinant polypeptides in the clinical pipeline typically lack stealth properties. We address this challenge by developing new unstructured polypeptides, called zwitterionic polypeptides (ZIPPs), that exhibit "stealth" behavior in vivo. We show that conjugating paclitaxel to a ZIPP imparts sufficient amphiphilicity to the polypeptide chain to drive its self-assembly into micelles, and increase its the half-life by 17-fold, and by 1.6-fold compared to non-stealth control. Treatment of mice bearing highly aggressive prostate or colon cancer with a single dose of ZIPP-paclitaxel nanoparticles leads to near-complete eradication of the tumor, and these nanoparticles have a wider therapeutic window than Abraxane-an FDA-approved taxane nanoformulation.