Biology subjects

Cohen, A.

Publications and source records attributed to Cohen, A..

34 records · Page 2Linked to original sources

bioRxiv2023

An experimental approach towards untangling the role of nature versus nurture in shaping the microbiome of social insects

The gut microbiota is intimately related to host wellbeing, in terms of physiology, immune function, and even social interactions. The strength of this relationship is dynamic, but the extent to which the microbiome is shaped by the identity of the host (nature) or its environment (nurture) remains largely unknown. Here we aimed to identify factors shaping the microbiomes of nursing workers and larvae of two Vespidae species, using a cross-species experimental design to control for effects of environment, host identity and their interactions. We found that the microbiome composition of adults depended principally on the environment. Conversely, larval microbiome composition differed more between host species, regardless of treatment. We also found distinct microbiota profiles between the two species, across life stages and independently. These findings further elucidate the complexity of the host-microbiome relationship shaped by the environment while retaining symbionts that benefit the host. These results suggest that holobiont evolution may have promoted the rise of social behavior in animals.

evolutionary biology↗

bioRxiv2023

Microcalcifications can either trigger or suppress breast precancer malignancy potential according to the mineral type in a 3D tumor model

Most early breast precancer lesions, termed ductal carcinoma in situ (DCIS), contain microcalcifications (MCs), which are calcium-containing pathological minerals. The most common type of MCs is calcium phosphate crystals, mainly carbonated apatite; it is associated with either benign or malignant lesions. In-vitro studies indicate that the crystal properties of apatite MCs can affect breast cancer progression. A less common type of MCs is calcium oxalate dihydrate (COD), which is almost always found in benign lesions. We developed a 3D tumor model of multicellular spheroids of human precancer cells containing synthetic MC analogs that link the crystal properties of MCs with the progression of breast precancer to invasive cancer. We show that apatite crystals induce proliferation and Her2 overexpression in DCIS cells. This tumor-triggering effect is increased when the carbonate fraction in the MCs decreases. COD crystals, in contrast, do not induce proliferation and reduce Her2 expression, even compared with control spheroids with no added MC analogs. This finding suggests that COD is not randomly located only in benign lesions--it may actively contribute to suppressing precancer progression in its surroundings. Our model provides an easy-to-manipulate platform to better understand the interactions between breast precancer cells and MCs. A better understanding of the effect of the crystal properties of MCs on precancer progression will potentially provide new directions for better precancer prognosis and treatment.

bioengineering↗

bioRxiv2022

Statistically unbiased prediction enables accurate denoising of voltage imaging data

Here we report SUPPORT (Statistically Unbiased Prediction utilizing sPatiOtempoRal information in imaging daTa), a self-supervised learning method for removing Poisson-Gaussian noise in voltage imaging data. SUPPORT is based on the insight that a pixel value in voltage imaging data is highly dependent on its spatially neighboring pixels in the same time frame, even when its temporally adjacent frames do not provide useful information for statistical prediction. Such spatiotemporal dependency is captured and utilized to accurately denoise voltage imaging data in which the existence of the action potential in a time frame cannot be inferred by the information in other frames. Through simulation and experiments, we show that SUPPORT enables precise denoising of voltage imaging data while preserving the underlying dynamics in the scene.

neuroscience↗

bioRxiv2022

Molecular-enriched functional connectivity in the human brain using multiband multi-echo simultaneous ASL/BOLD fMRI

Receptor-Enriched Analysis of functional Connectivity by Targets (REACT) is a novel analytical strategy that enriches functional connectivity (FC) information from functional MRI (fMRI) with molecular information on the neurotransmitter distribution density in the human brain, providing a biological basis to the FC analysis. So far, this integrative approach has been used in blood oxygen level-dependent (BOLD) fMRI studies only, providing new insights into the brain mechanisms underlying specific disorders and its response to pharmacological challenges. In this study, we demonstrate that the application of REACT can be further extended to arterial spin labelling (ASL) fMRI. Some of the advantages of this extension include the combination of neurotransmitter specific information provided by molecular imaging with a quantitative marker of neuronal activity, the suitability of ASL for pharmacological MRI (phMRI) studies assessing drug effects on baseline brain function, and the possibility to acquire images that are not affected by susceptibility artifacts in the regions linked to major neurotransmitter systems. In this work, we tested the feasibility of applying REACT to resting state ASL fMRI and compared the molecular-enriched FC maps derived from ASL data with those derived from BOLD data. We applied REACT to high-resolution, whole-brain simultaneous ASL/BOLD resting-state fMRI data of 29 healthy subjects and estimated the ASL- and BOLD-based FC maps related to six molecular systems, including the transporters of dopamine, noradrenaline, serotonin and vesicular acetylcholine, and the GABA-A and mGlu5 receptors. We then compared the ASL and BOLD FC maps in terms of spatial similarity, using the Dice Similarity Index and the voxel-wise spatial correlation. On a data subsample (N=19) we also evaluated the test-retest reproducibility of each modality using the regional intraclass correlation coefficient, and compared the two modalities. Our results showed robust spatial patterns of molecular-enriched functional connectivity for both modalities, moderate to high similarity between BOLD- and ASL-derived FC maps and mixed results in terms of reproducibility (i.e., none of the modalities outperformed the other). Overall, our findings show that the ASL signal is as informative as BOLD in detecting functional circuits associated with specific molecular pathways, and that the two modalities may provide complementary information related to these circuits. Considering the more direct link of ASL imaging with neuronal acrivity compared to BOLD and its suitability for phMRI studies, this new integrative approach could become a valuable asset in clinical studies investigating functional alterations in patients with brain disorders, or in pharmacological studies investigating the effects of new or existing compounds on the brain.

neuroscience↗

bioRxiv2022

ABA-IMPORTING TRANSPORTER 1.1 activity in the endosperm of tomato seeds restrains germination under salinity stress

The plant hormone abscisic acid (ABA) has a central role in the regulation of seed maturation and dormancy. ABA also restrains germination under abiotic-stress conditions. Here we show in tomato (Solanum lycopersicum) that the ABA importer ABA-IMPORTING TRANSPORTER 1.1 (AIT1.1) has a role in radicle emergence following imbibition. AIT1.1 expression was upregulated during imbibition, and CRISPR/Cas9-derived ait1.1 mutant seeds exhibited faster radicle emergence, increased germination and partial resistance to ABA. AIT1.1 was highly expressed in the endosperm, but not in the embryo, and ait1.1 isolated embryos did not show resistance to ABA. On the other hand, loss of AIT1.1 activity promoted the expression of endosperm-weakening related genes, and seed-coat scarification eliminated the promoting effect of ait1.1 on radicle emergence. Therefore, we propose that imbibition-induced AIT1.1 expression in the endosperm, mediates ABA-uptake into endosperm cells to restrain endosperm weakening. While salinity conditions strongly inhibited the wild-type (WT) M82 seed germination, it had much weaker effect on ait1.1 germination. We suggest that this AIT1.1 function was evolved to inhibit germination under unfavorable conditions, such as salinity. Unlike other ABA mutants, ait1.1 exhibited normal seed longevity, and therefore, the ait1.1 allele may have a potential for improving seed germination in crops.

plant biology↗

bioRxiv2022

Genome-scale CRISPR screening reveals that C3aR signaling is critical for rapid capture of fungi by macrophages

The fungal pathogen Histoplasma capsulatum (Hc) invades, replicates within, and destroys macrophages. To interrogate the molecular mechanisms underlying this interaction, we conducted a host-directed CRISPR-Cas9 screen and identified 361 genes that modify macrophage susceptibility to Hc infection, greatly expanding our understanding of host gene networks targeted by Hc. We identified pathways that have not been previously implicated in Hc interaction with macrophages, including the ragulator complex (involved in nutrient stress sensing), glycosylation enzymes, protein degradation machinery, mitochondrial respiration genes, solute transporters, and the ER membrane complex (EMC). The highest scoring protective hits included the complement C3a receptor (C3aR), a G-protein coupled receptor (GPCR) that recognizes the complement fragment C3a. Although it is known that the complement system reacts with the fungal surface, leading to opsonization and release of small peptide fragments such as C3a, a role for C3aR in macrophage susceptibility to fungi has not been elucidated. We demonstrated that whereas C3aR is dispensable for macrophage phagocytosis of bacteria and latex beads, it is critical for optimal macrophage capture of pathogenic fungi, including Hc, the ubiquitous fungal pathogen Candida albicans, and the causative agent of Valley Fever Coccidioides posadasii. We showed that C3aR localizes to the early phagosome during H. capsulatum infection where it coordinates the formation of actin-rich membrane protrusions that promote Hc capture. We also showed that the EMC promotes surface expression of C3aR, likely explaining its identification in our screen. Taken together, our results provide new insight into host processes that affect Hc-macrophage interactions and uncover a novel and specific role for C3aR in macrophage recognition of fungi.

microbiology↗

bioRxiv2021

Cooperative Allostery and Structural Dynamics of Streptavidin at Cryogenic- and Ambient-temperature

Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive protein that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric protein complexes. Also, it offers a versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, the first one is an ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7 [A] resolution and the second one is a cryogenic crystal structure (Apo-Cryo) at 1.1 [A] resolution. These structures are mostly in agreement with previous structural data. Combined with computational analysis, these structures provide invaluable information about structural dynamics of apo streptavidin. Collectively, these data further reveal a novel cooperative allostery of streptavidin which binds to substrate via water molecules that provide a polar interaction network and mimics the substrate biotin which displays one of the strongest affinities found in nature.

biophysics↗

bioRxiv2021

Reconstructing tumor trajectories during therapy through integration of multiple measurement modalities.

BackgroundAccurately determining changes in tumor size during therapy is essential to evaluating response or progression. However, individual imaging methodologies often poorly reflect pathologic response and long-term treatment efficacy in patients with estrogen receptor positive (ER+) early-stage breast cancer. Mathematical models that measure tumor progression over time by integrating diverse imaging and tumor measurement modalities are not currently used but could increase accuracy in measuring response and provide biological insights into cancer evolution. MethodsFor ER+ breast cancer patients enrolled on a neoadjuvant clinical trial, we reconstructed their tumor size trajectories during therapy by combining all available information on tumor size, including different imaging modalities, physical examinations and pathological assessment data. Tumor trajectories during six months of treatment were generated, using a Gaussian process and the most probable trajectories were evaluated, based on clinical data, using measurement models that account for biases and differences in precision between tumor measurement methods, such as MRI, ultrasound and mammograms. ResultsReconstruction of tumor trajectories during treatment identified five distinct patterns of tumor size changes, including rebound growth not evident from any single modality. These results increase specificity to distinguish innate or acquired resistance compared to using any single measurement alone. The speed of therapeutic response and extent of subsequent rebound tumor growth quantify sensitivity or resistance in this patient population. ConclusionsTumor trajectory reconstruction integrating multiple modalities of tumor measurement accurately describes tumor progression on therapy and reveals various patterns of patient responses. Mathematical models can integrate diverse response assessments and account for biases in tumor measurement, thereby providing insights into the timing and rate at which resistance emerges.

systems biology↗

bioRxiv2021

Large-scale quantification of human osteocyte lacunar morphological biomarkers as assessed by ultra-high-resolution desktop micro-computed tomography

Ultra-high-resolution imaging of the osteocyte lacuno-canalicular network (LCN) three-dimensionally (3D) in a high-throughput fashion has greatly improved the morphological knowledge about the constituent structures - positioning them as potential biomarkers. Technologies such as serial focused ion beam/scanning electron microscopy (FIB/SEM) and confocal scanning laser microscopy (CLSM) can image in extremely high resolution, yet only capture a small number of lacunae. Synchrotron radiation computed tomography (SR-CT) can image with both high resolution and high throughput but has a limited availability. Desktop micro-computed tomography (micro-CT) provides an attractive balance: high-throughput imaging on the micron level without the restrictions of SR-CT availability. Over the past decade, desktop micro-CT has been used to image osteocyte lacunae in a variety of animals, yet few studies have employed it to image human lacunae using clinical biopsies. In this study, accuracy, reproducibility, and sensitivity of large-scale quantification of human osteocyte lacunar morphometries were assessed by ultra-high-resolution desktop micro-computed tomography. For this purpose, thirty-one transiliac human bone biopsies containing trabecular and cortical regions were imaged using ultra-high-resolution desktop micro-CT at a nominal isotropic voxel resolution of 1.2m. The resulting 3D images were segmented, component labeled, and the following morphometric parameters of 7.71 million lacunae were measured: Lacunar number (Lc.N), density (Lc.N/BV), porosity (Lc.TV/BV), volume (Lc.V), surface area (Lc.S), surface area to volume ratio (Lc.S/Lc.V), stretch (Lc.St), oblateness (Lc.Ob), sphericity (Lc.Sr), equancy (Lc.Eq), and angle (Lc.{theta}). Accuracy was quantified by comparing automated lacunar identification to manual identification. Mean true positive rate (TPR), false positive rate (FPR), and false negative rate (FNR) were 89.0%, 3.4%, and 11.0%, respectively. Regarding the reproducibility of lacunar morphometry from repeated measurements, precision errors were low (0.2 - 3.0%) and intraclass correlation coefficients were high (0.960 - 0.999). Significant differences between cortical and trabecular regions (p<0.001) existed for Lc.N/BV, Lc.TV/BV, local lacunar surface area ( ), and local lacunar volume ( ), all of which demonstrate the sensitivity of the method and are possible biomarker candidates. This study provides the foundation required for future large-scale morphometric studies using ultra-high-resolution desktop micro-CT and high-throughput analysis of millions of osteocyte lacunae in human bone samples. Furthermore, the validation of this technology for imaging of human lacunar properties establishes the quality and reliability required for the accurate, precise, and sensitive assessment of osteocyte morphometry in clinical bone biopsies.

bioengineering↗

bioRxiv2020

Thinking ahead: prediction in context as a keystone of language in humans and machines

Departing from traditional linguistic models, advances in deep learning have resulted in a new type of predictive (autoregressive) deep language models (DLMs). Using a self-supervised next-word prediction task, these models are trained to generate appropriate linguistic responses in a given context. We provide empirical evidence that the human brain and autoregressive DLMs share three fundamental computational principles as they process natural language: 1) both are engaged in continuous next-word prediction before word-onset; 2) both match their pre-onset predictions to the incoming word to calculate post-onset surprise (i.e., prediction error signals); 3) both represent words as a function of the previous context. In support of these three principles, our findings indicate that: a) the neural activity before word-onset contains context-dependent predictive information about forthcoming words, even hundreds of milliseconds before the words are perceived; b) the neural activity after word-onset reflects the surprise level and prediction error; and c) autoregressive DLM contextual embeddings capture the neural representation of context-specific word meaning better than arbitrary or static semantic embeddings. Together, our findings suggest that autoregressive DLMs provide a novel and biologically feasible computational framework for studying the neural basis of language.

neuroscience↗

bioRxiv2020

Lipidome profiles of plasma microvesicles differ in experimental cerebral malaria, compared to malaria without neurological complications

Cerebral malaria (CM), a fatal complication of Plasmodium infection that affects children in sub-Saharan Africa and adults in South-East Asia, results from incompletely understood pathogenetic mechanisms, which include an excessive release of microvesicles (MV). Plasma MV levels have been found elevated in CM patients and in the experimental mouse model. We compared lipid profiles in circulating MV purified from CBA mice infected with P. berghei ANKA (PbA), which causes CM, to those from P. yoelii (Py), which does not. Here we show that plasma MV produced at the time of CM differed dramatically from those from non-CM mice, in spite of identical levels of parasitaemia. Using high-resolution LCMS, we identified over 300 lipid species within 12 lipid classes. Total lysophosphatidylethanolamine (LPE) levels were significantly lower in PbA infection compared to uninfected mice, while they were unchanged in Py MV, and lysophosphatidylcholine (LPC) was more significantly reduced in PbA mice compared to the other two groups. These results suggest, for the time, that experimental CM is characterised by specific changes in lipid composition of circulating MV, pointing towards triglycerides (TG) especially docosahexaenoic acid (DHA 22:6) containing species, phosphatidylethanolamine (PE), LPC, LPE, and diacylglycerol (DG) as potential important players in CM pathogenesis.

pathology↗

bioRxiv2020

Neural synchrony predicts children's learning of novel words

Social interactions have a well-studied influence on early development and language learning. Recent work has begun to investigate the neural mechanisms that underlie shared representations of input, documenting neural synchrony or coupling (measured using intersubject temporal correlations of neural activity) between individuals exposed to the same stimulus. Neural synchrony has been found to predict the quality of engagement with a stimulus and with communicative cues, but studies have yet to address how neural synchrony among children may relate to real-time learning. Using functional near-infrared spectroscopy (fNIRS), we recorded the neural activity of 45 children (3.5-4.5 years) during joint book reading with an adult experimenter. The custom childrens book contained four novel words and objects embedded in an unfolding story, as well as a range of narrative details about object functions and character roles. We observed synchronized neural activity between child participants during book reading and found a positive correlation between learning and intersubject neural synchronization in parietal cortex, an area implicated in narrative-level processing in adult research. Our findings suggest that childrens learning is facilitated by active neural engagement with the dynamics of natural social input.

neuroscience↗

bioRxiv2020

Production of Hyaluronan by the Trophectoderm is a Prerequisite for Mouse Blastocyst Attachment

Embryo implantation requires execution of highly synchronized processes at the feto-maternal interface, initiated by blastocyst attachment to the endometrial epithelium. Hyaluronan is a major ECM component known to regulate adhesion-associated biological processes in various physiological settings. We hypothesized that hyaluronan may facilitate blastocyst attachment. In order to test our hypothesis, we characterized the blastocyst expression of hyaluronan synthesizing and degrading enzymes, as well as the expression of hyaluronan receptors during attachment. The functional impact of hyaluronan was challenged by the use of mouse transgenic blastocysts, in which genes encoding for hyaluronan synthesizing enzymes were deleted using lentiviral incorporation of Cas-9 endonuclease alongside specific short-guide RNAs into the embryonic trophectoderm. Embryos with transgenic trophectoderm were tested for their attachment in vitro, or assessed for implantation in vivo, upon transfer to foster dams. Deletion of the trophectoderm hyaluronan biosynthesis significantly reduced the number of blastocysts attached to human uterine epithelium cells in vitro. Reduced attachment was also observed in vivo, in pregnant mice carrying blastocysts with hyaluronan-depleted trophectoderm. In agreement, trophectoderm expression of osteopontin, was downregulated upon depletion of hyaluronan. MRI measurements revealed a decrease in uterine blood vessels permeability. Uterine expression of VEGF-A, PTGS-2 and uterine osteopontin, which constitute the immediate response to blastocyst attachment was also reduced. Furthermore, impaired implantation, associated with a decrease in hyaluronan synthesis in the mural trophectoderm, obtained upon tamoxifen treatment, has been recovered by LIF administration. These results demonstrate that estrogen-regulated hyaluronan-synthesis in the trophectoderm is indispensable for mouse blastocysts attachment to the uterine epithelium.

developmental biology↗

bioRxiv2020

Hyaluronan-NK cell Interaction Controls the Primary Vascular Barrier during Early Pregnancy

Successful implantation is associated with a unique spatial pattern of vascular remodeling, characterized by profound peripheral neo-vascularization surrounding a peri-embryo avascular niche. We hypothesized that hyaluronan controls the formation of the unique vascular pattern encompassing the embryo. This hypothesis was evaluated by genetic modification of hyaluronan metabolism specifically targeted to embryonic trophoblast cells. The outcome of altered hyaluronan deposition on uterine vascular remodeling and post-implantation development were analyzed by MRI, detailed histological examinations, and RNA-sequencing of uterine NK cells. Our experiments revealed that eliminating the anti-angiogenic hyaluronan, led to elevated expression of MMP-9, VEGF-A and its receptor VEGFR-2, accompanied by reduced recruitment of uterine NK cells. Further local decrease in VEGFR-3 resulted in impaired formation of vascular sinuous folds, ectopic angiogenesis and dysfunctional uterine NK cells. Conversely, enhanced deposition of hyaluronan caused the expansion of the maternal-embryo barrier, leading to an increased diffusion distance and aborted implantation. These results demonstrate a pivotal role for hyaluronan in successful pregnancy by fine-tuning the peri-embryo avascular niche and maternal vascular morphogenesis.

developmental biology↗

bioRxiv2020

Multimodal magnetic resonance imaging predicts regional amyloid-β burden in the brain

Alzheimers disease (AD) is the most common cause of dementia and identifying early markers of this disease is important for prevention and treatment strategies. Amyloid - {beta} protein deposition is one of the earliest detectable pathological changes in AD. But in-vivo detection of amyloid - {beta} using positron emission tomography (PET) is hampered by high cost and limited geographical accessibility. These factors can become limiting when PET is used to screen large numbers of subjects into prevention trials when only a minority are expected to be amyloid- {beta} - positive. Structural MRI is advantageous; as it is relatively inexpensive and more accessible. Thus it could be widely used in large studies, even when frequent or repetitive imaging is necessary. We used a machine learning, pattern recognition, approach using intensity-based features from individual and combination of MR modalities (T1 weighted, T2 weighted, T2 fluid attenuated inversion recovery [FLAIR], susceptibility weighted imaging) to predict voxel-level amyloid- {beta} in the brain. The MR- amyloid {beta} relation was learned within each subject and generalized across subjects using subject-specific features (demographic, clinical, and summary MR features). When compared to other modalities, combination of T1-weighted, T2-weighted FLAIR, and SWI performed best in predicting the amyloid- {beta} status as positive or negative. T2- weighted performed the best in predicting change in amyloid- {beta} over two timepoints. Overall, our results show feasibility of amyloid- {beta} prediction by MRI.

bioengineering↗

bioRxiv2019

Guanine content of microRNAs is associated with their tumor suppressive and oncogenic roles in lung and breast cancers

BackgroundmicroRNAs (miRNAs, miRs) are small noncoding RNAs that negatively regulate gene expression at the post-transcriptional level and fine-tune gene functions. A global repression of miRNAs expression in different types of human tumors, after exposure to cigarette-smoke, or to the hormone estrogen, have been shown to be associated with guanine (G) enrichment in the terminal loops (TLs) of their precursors. Methodswe integrated the G content of miRNA mature forms and precursor miRNA TLs with their described function in the literature, using the PubMed database. Gene Ontology term analysis was used to describe the pathways in which the G-enriched miRNA targets are involved. Resultswe show here an association between the relative G enrichment of precursor miRNAs TLs and their tendency to act as tumor suppressor miRs in human lung and breast cancers. Another association was observed between the high G content of the miRNAs 5-mature forms and their tendency to act as oncomiRs. Conclusionsthe results support previous findings showing that the G sequence content is an important feature determining miRNA expression and function, and open the way for future cancer investigations in this direction.

cancer biology↗