A Cu3BHT-Graphene van der Waals Heterostructure with Strong Interlayer Coupling for Highly Efficient Photoinduced Charge Separation

Two-dimensional van der Waals heterostructures (2D vdWhs) are of significant interest due to their intriguing physical properties critically defined by the constituent monolayers and their interlayer coupling. Synthetic access to 2D vdWhs based on chemically tunable monolayer organic 2D materials remains challenging. Herein, the fabrication of a novel organic-inorganic bilayer vdWh by combining π-conjugated 2D coordination polymer (2DCP, i.e., Cu3BHT, BHT = benzenehexathiol) with graphene is reported. Monolayer Cu3BHT with detectable µm2-scale uniformity and atomic flatness is synthesized using on-water surface chemistry. A combination of diffraction and imaging techniques enables the determination of the crystal structure of monolayer Cu3BHT with atomic precision. Leveraging the strong interlayer coupling, Cu3BHT-graphene vdWh exhibits highly efficient photoinduced interlayer charge separation with a net electron transfer efficiency of up to 34% from Cu3BHT to graphene, superior to those of reported bilayer 2D vdWhs and molecular-graphene vdWhs. This study unveils the potential for developing novel 2DCP-based vdWhs with intriguing physical properties.

Chromosomal Inversions and the Demography of Speciation in Drosophila montana and Drosophila flavomontana

Chromosomal inversions may play a central role in speciation given their ability to locally reduce recombination and therefore genetic exchange between diverging populations. We analyzed long- and short-read whole-genome data from sympatric and allopatric populations of 2 Drosophila virilis group species, Drosophila montana and Drosophila flavomontana, to understand if inversions have contributed to their divergence. We identified 3 large alternatively fixed inversions on the X chromosome and one on each of the autosomes 4 and 5. A comparison of demographic models estimated for inverted and noninverted (colinear) chromosomal regions suggests that these inversions arose before the time of the species split. We detected a low rate of interspecific gene flow (introgression) from D. montana to D. flavomontana, which was further reduced inside inversions and was lower in allopatric than in sympatric populations. Together, these results suggest that the inversions were already present in the common ancestral population and that gene exchange between the sister taxa was reduced within inversions both before and after the onset of species divergence. Such ancestrally polymorphic inversions may foster speciation by allowing the accumulation of genetic divergence in loci involved in adaptation and reproductive isolation inside inversions early in the speciation process, while gene exchange at colinear regions continues until the evolving reproductive barriers complete speciation. The overlapping X inversions are particularly good candidates for driving the speciation process of D. montana and D. flavomontana, since they harbor strong genetic incompatibilities that were detected in a recent study of experimental introgression.

Race and statistics in facial recognition: Producing types, physical attributes, and genealogies

Principal component analysis (PCA) is a common statistical procedure. In forensics, it is used in facial recognition technologies and composite sketching systems. PCA is especially helpful in contexts with high facial diversity, which is often translated as racial diversity. In these settings, researchers use PCA to define a 'normal face' and organize the rest of the available facial diversity based on their resemblance to or difference from that norm. In this way, the use of PCA introduces an 'ontology of the normal' in which expectations about how a normal face should look are corroborated by statistical calculations of normality. I argue that the use of PCA can lead to a statistical reification of racial stereotypes that informs recognition practices. I discuss current and historical cases in which PCA is used: one of face perception theorization ('face space theory') and two of technology development (the 'eigenfaces' facial recognition algorithm and the 'EvoFIT' composite sketching system). In each, PCA aligns facial normality with racial expectations, and instrumentalizes race in specific ways: as a type, physical attribute, or genealogy. This analysis of PCA does two things. First, it opens the black box of facial recognition to uncover how stereotypes and intuitions about normality become part of theories and technologies of facial recognition. Second, it explains why racial categorizations remain central in contemporary identification technologies and other forensic practices.

Differential Effects of Erythropoietin Administration and Overexpression on Venous Thrombosis in Mice

BACKGROUND

 Deep vein thrombosis (DVT) is a common condition associated with significant mortality due to pulmonary embolism. Despite advanced prevention and anticoagulation therapy, the incidence of venous thromboembolism remains unchanged. Individuals with elevated hematocrit and/or excessively high erythropoietin (EPO) serum levels are particularly susceptible to DVT formation. We investigated the influence of short-term EPO administration compared to chronic EPO overproduction on DVT development. Additionally, we examined the role of the spleen in this context and assessed its impact on thrombus composition.

METHODS

 We induced ligation of the caudal vena cava (VCC) in EPO-overproducing Tg(EPO) mice as well as wildtype mice treated with EPO for two weeks, both with and without splenectomy. The effect on platelet circulation time was evaluated through FACS analysis, and thrombus composition was analyzed using immunohistology.

RESULTS

 We present evidence for an elevated thrombogenic phenotype resulting from chronic EPO overproduction, achieved by combining an EPO-overexpressing mouse model with experimental DVT induction. This increased thrombotic state is largely independent of traditional contributors to DVT, such as neutrophils and platelets. Notably, the pronounced prothrombotic effect of red blood cells (RBCs) only manifests during chronic EPO overproduction and is not influenced by splenic RBC clearance, as demonstrated by splenectomy. In contrast, short-term EPO treatment does not induce thrombogenesis in mice. Consequently, our findings support the existence of a differential thrombogenic effect between chronic enhanced erythropoiesis and exogenous EPO administration.

CONCLUSION

 Chronic EPO overproduction significantly increases the risk of DVT, while short-term EPO treatment does not. These findings underscore the importance of considering EPO-related factors in DVT risk assessment and potential therapeutic strategies.

Timing of physical activity in relation to liver fat content and insulin resistance

AIMS/HYPOTHESIS

We hypothesised that the insulin-sensitising effect of physical activity depends on the timing of the activity. Here, we examined cross-sectional associations of breaks in sedentary time and timing of physical activity with liver fat content and insulin resistance in a Dutch cohort.

METHODS

In 775 participants of the Netherlands Epidemiology of Obesity (NEO) study, we assessed sedentary time, breaks in sedentary time and different intensities of physical activity using activity sensors, and liver fat content by magnetic resonance spectroscopy (n=256). Participants were categorised as being most active in the morning (06:00-12:00 hours), afternoon (12:00-18:00 hours) or evening (18:00-00:00 hours) or as engaging in moderate-to-vigorous-physical activity (MVPA) evenly distributed throughout the day. Most active in a certain time block was defined as spending the majority (%) of total daily MVPA in that block. We examined associations between sedentary time, breaks and timing of MVPA with liver fat content and HOMA-IR using linear regression analyses, adjusted for demographic and lifestyle factors including total body fat. Associations of timing of MVPA were additionally adjusted for total MVPA.

RESULTS

The participants (42% men) had a mean (SD) age of 56 (4) years and a mean (SD) BMI of 26.2 (4.1) kg/m². Total sedentary time was not associated with liver fat content or insulin resistance, whereas the amount of breaks in sedentary time was associated with higher liver fat content. Total MVPA (-5%/h [95% CI -10%/h, 0%/h]) and timing of MVPA were associated with reduced insulin resistance but not with liver fat content. Compared with participants who had an even distribution of MVPA throughout the day, insulin resistance was similar (-3% [95% CI -25%, 16%]) in those most active in morning, whereas it was reduced in participants who were most active in the afternoon (-18% [95% CI -33%, -2%]) or evening (-25% [95% CI -49%, -4%]).

CONCLUSIONS/INTERPRETATION

The number of daily breaks in sedentary time was not associated with lower liver fat content or reduced insulin resistance. Moderate-to-vigorous activity in the afternoon or evening was associated with a reduction of up to 25% in insulin resistance. Further studies should assess whether timing of physical activity is also important for the occurrence of type 2 diabetes.

Graph-based algorithms for Laplace transformed coalescence time distributions

Extracting information on the selective and demographic past of populations that is contained in samples of genome sequences requires a description of the distribution of the underlying genealogies. Using the Laplace transform, this distribution can be generated with a simple recursive procedure, regardless of model complexity. Assuming an infinite-sites mutation model, the probability of observing specific configurations of linked variants within small haplotype blocks can be recovered from the Laplace transform of the joint distribution of branch lengths. However, the repeated differentiation required to compute these probabilities has proven to be a serious computational bottleneck in earlier implementations.

Here, I show that the state space diagram can be turned into a computational graph, allowing efficient evaluation of the Laplace transform by means of a graph traversal algorithm. This general algorithm can, for example, be applied to tabulate the likelihoods of mutational configurations in non-recombining blocks. This work provides a crucial speed up for existing composite likelihood approaches that rely on the joint distribution of branch lengths to fit isolation with migration models and estimate the parameters of selective sweeps. The associated software is available as an open-source Python library, agemo.

For simple models of idealised populations, the process that generates the observed sequences can be mathematically described. For a given number of samples, we can enumerate all possible genealogies. We can even incorporate the impact of past events like population size reductions on the observed sequence variation. However, the number of possible genealogies will become very large, very fast. So, to extract information from the observed mutations, we need mathematical tools and efficient algorithms to use the information contained within the large collection of possible genealogies.

The Laplace transform is one such mathematical tool that allows us to recursively generate the branch length distribution of all genealogies. Here I show how the transform can be represented as a graph. Using this nonlinear data structure, I define a general procedure to efficiently evaluate the associated mathematical expressions. And I further show how this can be used to speed up existing composite likelihood approaches to fit demographic models and estimate sweep parameters. The associated software, agemo, has a well-documented Python API and has been designed with extensibility in mind, making it an ideal back-end for many other inference approaches in population genetics.

Serum sex hormone-binding globulin levels are reduced and inversely associated with intrahepatic lipid content and saturated fatty acid fraction in adult patients with glycogen storage disease type 1a

PURPOSE

De novo lipogenesis has been inversely associated with serum sex hormone-binding globulin (SHBG) levels. However, the directionality of this association has remained uncertain. We, therefore, studied individuals with glycogen storage disease type 1a (GSD1a), who are characterized by a genetic defect in glucose-6-phosphatase resulting in increased rates of de novo lipogenesis, to assess the downstream effect on serum SHBG levels.

METHODS

A case-control study comparing serum SHBG levels in patients with GSD1a (n = 10) and controls matched for age, sex, and BMI (n = 10). Intrahepatic lipid content and saturated fatty acid fraction were quantified by proton magnetic resonance spectroscopy.

RESULTS

Serum SHBG levels were statistically significantly lower in patients with GSD1a compared to the controls (p = 0.041), while intrahepatic lipid content and intrahepatic saturated fatty acid fraction-a marker of de novo lipogenesis-were significantly higher in patients with GSD1a (p = 0.001 and p = 0.019, respectively). In addition, there was a statistically significant, inverse association of intrahepatic lipid content and saturated fatty acid fraction with serum SHBG levels in patients and controls combined (β: - 0.28, 95% CI: - 0.47;- 0.09 and β: - 0.02, 95% CI: - 0.04;- 0.01, respectively).

CONCLUSION

Patients with GSD1a, who are characterized by genetically determined higher rates of de novo lipogenesis, have lower serum SHBG levels than controls.

Multiscale imaging of therapeutic anti-PD-L1 antibody localization using molecularly defined imaging agents

BACKGROUND

While immune checkpoint inhibitors such as anti-PD-L1 antibodies have revolutionized cancer treatment, only subgroups of patients show durable responses. Insight in the relation between clinical response, PD-L1 expression and intratumoral localization of PD-L1 therapeutics could improve patient stratification. Therefore, we present the modular synthesis of multimodal antibody-based imaging tools for multiscale imaging of PD-L1 to study intratumoral distribution of PD-L1 therapeutics.

RESULTS

To introduce imaging modalities, a peptide containing a near-infrared dye (sulfo-Cy5), a chelator (DTPA), an azide, and a sortase-recognition motif was synthesized. This peptide and a non-fluorescent intermediate were used for site-specific functionalization of c-terminally sortaggable mouse IgG1 (mIgG1) and Fab anti-PD-L1. To increase the half-life of the Fab fragment, a 20 kDa PEG chain was attached via strain-promoted azide-alkyne cycloaddition (SPAAC). Biodistribution and imaging studies were performed with 111In-labeled constructs in 4T1 tumor-bearing mice. Comparing our site-specific antibody-conjugates with randomly conjugated antibodies, we found that antibody clone, isotype and method of DTPA conjugation did not change tumor uptake. Furthermore, addition of sulfo-Cy5 did not affect the biodistribution. PEGylated Fab fragment displayed a significantly longer half-life compared to unPEGylated Fab and demonstrated the highest overall tumor uptake of all constructs. PD-L1 in tumors was clearly visualized by SPECT/CT, as well as whole body fluorescence imaging. Immunohistochemistry staining of tumor sections demonstrated that PD-L1 co-localized with the fluorescent and autoradiographic signal. Intratumoral localization of the imaging agent could be determined with cellular resolution using fluorescent microscopy.

CONCLUSIONS

A set of molecularly defined multimodal antibody-based PD-L1 imaging agents were synthesized and validated for multiscale monitoring of PD-L1 expression and localization. Our modular approach for site-specific functionalization could easily be adapted to other targets.

Leaf Apoplast of Field-Grown Potato Analyzed by Quantitative Proteomics and Activity-Based Protein Profiling

Multiple biotic and abiotic stresses challenge plants growing in agricultural fields. Most molecular studies have aimed to understand plant responses to challenges under controlled conditions. However, studies on field-grown plants are scarce, limiting application of the findings in agricultural conditions. In this study, we investigated the composition of apoplastic proteomes of potato cultivar Bintje grown under field conditions, i.e., two field sites in June-August across two years and fungicide treated and untreated, using quantitative proteomics, as well as its activity using activity-based protein profiling (ABPP). Samples were clustered and some proteins showed significant intensity and activity differences, based on their field site and sampling time (June-August), indicating differential regulation of certain proteins in response to environmental or developmental factors. Peroxidases, class II chitinases, pectinesterases, and osmotins were among the proteins more abundant later in the growing season (July-August) as compared to early in the season (June). We did not detect significant differences between fungicide Shirlan treated and untreated field samples in two growing seasons. Using ABPP, we showed differential activity of serine hydrolases and β-glycosidases under greenhouse and field conditions and across a growing season. Furthermore, the activity of serine hydrolases and β-glycosidases, including proteins related to biotic stress tolerance, decreased as the season progressed. The generated proteomics data would facilitate further studies aiming at understanding mechanisms of molecular plant physiology in agricultural fields and help applying effective strategies to mitigate biotic and abiotic stresses.

Characterization of Long Non-Coding RNAs in Systemic Sclerosis Monocytes: A Potential Role for PSMB8-AS1 in Altered Cytokine Secretion

Systemic sclerosis (SSc) is a chronic autoimmune disease mainly affecting the connective tissue. In SSc patients, monocytes are increased in circulation, infiltrate affected tissues, and show a pro-inflammatory activation status, including the so-called interferon (IFN) signature. We previously demonstrated that the dysregulation of the IFN response in SSc monocytes is sustained by altered epigenetic factors as well as by upregulation of the long non-coding RNA (lncRNA) NRIR. Considering the enormously diverse molecular functions of lncRNAs in immune regulation, the present study investigated the genome-wide profile of lncRNAs in SSc monocytes, with the aim to further unravel their possible role in monocyte dysregulation and disease pathogenesis. Transcriptomic data from two independent cohorts of SSc patients identified 886 lncRNAs with an altered expression in SSc monocytes. Differentially expressed lncRNAs were correlated with neighboring protein coding genes implicated in the regulation of IFN responses and apoptotic signaling in SSc monocytes. In parallel, gene co-expression network analysis identified the lncRNA PSMB8-AS1 as a top-ranking hub gene in co-expression modules implicated in cell activation and response to viral and external stimuli. Functional characterization of PSMB8-AS1 in monocytes demonstrated that this lncRNA is involved in the secretion of IL-6 and TNFα, two pivotal pro-inflammatory cytokines altered in the circulation of SSc patients and associated with fibrosis and disease severity. Collectively, our data showed that lncRNAs are linked to monocyte dysregulation in SSc, and highlight their potential contribution to disease pathogenesis.

Gut Microbiota and Host Juvenile Growth

Good genes, good food, good friends. That is what parents hope will sustain and nurture the harmonious growth of their children. The impact of the genetic background and nutrition on postnatal growth has been in the spot light for long, but the good friends have come to the scene only recently. Among the good friends perhaps the most crucial ones are those that we are carrying within ourselves. They comprise the trillions of microbes that collectively constitute each individual's intestinal microbiota. Indeed, recent epidemiological and field studies in humans, supported by extensive experimental data on animal models, demonstrate a clear role of the intestinal microbiota on their host's juvenile growth, especially under suboptimal nutrient conditions. Genuinely integrative approaches applicable to invertebrate and vertebrate systems combine tools from genetics, developmental biology, microbiology, nutrition, and physiology to reveal how gut microbiota affects growth both positively and negatively, in healthy and pathological conditions. It appears that certain natural or engineered gut microbiota communities can positively impact insulin/IGF-1 and steroid hormone signaling, thus contributing to the host juvenile development and maturation.

The role of the two splice variants and extranuclear pathway on Ki-67 regulation in non-cancer and cancer cells

Ki-67 is a nuclear protein that has been used in cancer diagnostic because of its specific cell-cycle dependent expression profile. After quantifying and characterising the expression level of Ki-67, as a function of the cell cycle, we found out that the two main splice variants of the protein (i.e. α and β) are differently regulated in non-cancerous and cancerous cells both at mRNA and protein level. We were able to correlate the presence of the α variant of the protein with the progression through the interphase of cell cycle. We also observed that the different expression profiles correspond to different degradation pathways for non-cancerous and cancerous cells. Furthermore, Ki-67 is continuously regulated and degraded via proteasome system in both cell types, suggesting an active control of the protein. However we also observed a putative extranuclear elimination pathway of Ki-67 where it is transported to the Golgi apparatus. Our evidence in the different expression of the splice variants may represent a milestone for the development of new targets for cancer diagnostic and prognostic. Additionally, the unexpected extranuclear elimination of Ki-67 strongly suggests that this protein must be looked at also outside of the "nuclear box", as thought to date.

A systematic review and meta-analysis of the seroprevalence of Toxoplasma gondii in cats in mainland China

BACKGROUND

Toxoplasmosis is caused by Toxoplasma gondii which can infect all warm-blooded animals. As the most common feline definitive host, cats play a vital role in the transmission of T. gondii. However, national estimates of the seroprevalence of T. gondii in cats in mainland China are lacking, and therefore a systematic review and meta-analysis were performed to provide insight into national environmental transmission levels and potential transmission to humans.

METHODS

Studies published up until July 1, 2016, on T. gondii seroprevalence in cats within mainland China were searched for in CNKI, WanFang, CBM, PubMed, Embase and through the reference lists of resulting articles. The seroprevalence with its 95% confidence interval (CI) for each individual study was presented, and then point estimates and their 95% confidence intervals (CIs) of pooled seroprevalence were calculated. Subgroup analyses were performed according to potential risk factors.

RESULTS

A total of 38 eligible studies, published between 1995 to 2016, covering fifteen provinces and municipalities, and involving 7,285 cats, were included. The seroprevalence in cats per study ranged from 3.9 to 79.4% with a median of 20.3%. As substantial heterogeneity existed among studies, a random-effects model was used to estimate the pooled seroprevalence. The value of the point estimate seroprevalence was 24.5% (95% CI: 20.1-29.0). Seroprevalence in stray cats was significantly higher than in pet cats (OR = 3.00, 95% CI: 1.60-5.64). The seroprevalence increased significantly with cat age (P = 0.018) with 17.4% (95% CI: 7.6-27.2) in the group of ≤ 1 year old, 19.5% (95% CI: 12.7-26.3) in the group of ≤ 3 year-old and 31.6% (95% CI: 22.9-40.3) in the group of > 3 year-old.

CONCLUSIONS

The seroprevalence of T. gondii in cats in mainland China was moderate and was associated with cat ownership and age. Due to the increasing prevalence of pet cats in China and the intimate relationship between these cats and humans, this might present a significant exposure risk, particularly for China's large susceptible population. Therefore, further research is needed into the links between cat ownership and human T. gondii infection and how to reduce T. gondii exposure in humans via cat contacts and the environmental contamination with T. gondii oocysts by cats.

The Actin Filament-Binding Protein Coronin Regulates Motility in Plasmodium Sporozoites

Parasites causing malaria need to migrate in order to penetrate tissue barriers and enter host cells. Here we show that the actin filament-binding protein coronin regulates gliding motility in Plasmodium berghei sporozoites, the highly motile forms of a rodent malaria-causing parasite transmitted by mosquitoes. Parasites lacking coronin show motility defects that impair colonization of the mosquito salivary glands but not migration in the skin, yet result in decreased transmission efficiency. In non-motile sporozoites low calcium concentrations mediate actin-independent coronin localization to the periphery. Engagement of extracellular ligands triggers an intracellular calcium release followed by the actin-dependent relocalization of coronin to the rear and initiation of motility. Mutational analysis and imaging suggest that coronin organizes actin filaments for productive motility. Using coronin-mCherry as a marker for the presence of actin filaments we found that protein kinase A contributes to actin filament disassembly. We finally speculate that calcium and cAMP-mediated signaling regulate a switch from rapid parasite motility to host cell invasion by differentially influencing actin dynamics.

Parasites causing malaria are transmitted by mosquitoes and need to migrate to cross tissue barriers. The form of the parasite transmitted by the mosquito, the so-called sporozoite, needs motility to enter the salivary glands, to migrate within the skin and to enter into blood capillaries and eventually hepatocytes, where the parasites differentiate into thousands of merozoites that invade red blood cells. Sporozoite motility is based on an actin-myosin motor, as is the case in many other eukaryotic cells. However, most eukaryotic cells move much slower than sporozoites. How these parasites reach their high speed is not clear but current evidence suggests that actin filaments need to be organized by either actin-binding proteins or membrane proteins that link the filaments to an extracellular substrate.

The present study explores the role of the actin filament-binding protein coronin in the motility of sporozoites of the rodent model parasite Plasmodium berghei. We found that the deletion of P. berghei coronin leads to defects in parasite motility and thus lower infection of mosquito salivary glands, which translates into less efficient transmission of the parasites. Our experiments suggest that coronin organizes actin filaments to achieve rapid and directional motility. We also identify two signaling pathways that converge to regulate actin filament dynamics and suggest that they play a role in switching the parasite from its motility mode to a cell invasion mode.