bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of point density on interpretability of lidar-derived forest structure metrics in two temperate forests
Authors: Swanson A. Christine , Merrick Trina , Abelev Andrei , Liang Robert , Vermillion Michael , Buma Willibroad , Li Rong-Rong
Published: January 2024

Three-dimensional forest structure plays an important role in processes such as biomass accumulation and fire spread and provides wildlife with habitat and foraging spaces. Advances in lidar mapping have improved forest structure quantification at local to global scales. However, point cloud density may have effects on estimates of forest structure variables that are not well understood and may vary by forest structural type (e.g. closed vs open canopy). In this study we investigated the effects of lidar point cloud density on forest structure parametrization in an open canopy pine-dominated forest at Assateague Island National Seashore (AINS) and a closed-canopy mixed hardwood temperate forest at the Keweenaw Research Center (KRC) using uncrewed aerial system (UAS)-based lidar. We decimated high point density (> 1000 points m-2) lidar data to between 1 and 175 points m-2and analyzed 26 forest structure metrics using Tukey’s method, reliability ratio, and correlation analyses.

Effects of point density on forest structure parameters were often site-dependent, as anticipated. At AINS, maximum (zmax) and mode (zmode) height significantly differed for point densities less than 10 pts m-2and 25 points m-2, respectively, while at KRC, the thresholds were 75 points m-2forzmaxand 50 points m-2forzmode. Reliability ratio ofzmax, height skewness, height quantiles, and the coefficient of variation of mean leaf area density (LAD) also varied dependent on point density at AINS. At both sites, metrics related LAD varied significantly (p < 0.001) at all but the highest point densities, and the reliability ratio forzmode, kurtosis of height distribution and mean horizontal coefficient of variation of LAD varied across point densities without any clear pattern. Point density mainly affected correlations between LAD-derived structural metrics and other metrics (e.g., as point density increased, Shannon diversity of LAD changed from being positively to negatively correlated tozmax). This study demonstrates how point density differentially affects lidar-derived forest structure parameters in diverse forest types. Scientists must understand these effects to interpret and compare forest structure attributes derived from different lidars.
Harnessing the power of poplar tree natural genetic variation for the development of future sustainable biofuels and bioproducts: a droughted marginal-land experiment for multi-disciplinary investigations
Authors: Taylor Gail , Bailey-Bale Jack H , Klein Marie C , Milner Suzanne , Chen Jin-Gui , Muchero Wellington , Freer-Smith Peter , Tschaplinski Timothy J. , Tuskan Jerry
Published: January 2024

The emerging bioeconomy offers significant potential to replace fossil-fuel-based energy, manufacturing, and processing with that utilizing biomass as the raw feedstock. However, feedstock production from non-food crops such as fast-growing trees, must be delivered at scale, in a reliable and consistent manner, utilizing marginal land unsuitable for food crops and with minimum inputs. This new generation of feedstock crops has a limited history of domestication. Foundational knowledge is required to enable rapid selection and breeding for improved cultivars and varieties to enable large-scale planting of 600M ha, globally over the coming decades. Here, we describe an innovative field platform with over 1,000 unique genotypes of fast-growing poplar (Populus trichocarpa) trees, each sequenced and being subjected to a controlled drought. The 6.5 ha site provides opportunities to bring together multi-disciplinary phenotyping science linked to computational, and AI approaches, enabling the link between complex plant traits and their underlying genes to be rapidly established and translated into the development of improved climate-resilient germplasm for a future at-scale bioeconomy.
Species delimitation analysis indicates cryptic speciation forTerpios gelatinosus(Porifera, Demospongiae) from coastal regions of the northeastern Mediterranean Sea
Authors: Öztürk Esra , Temiz Berivan , Karahan Arzu
Published: January 2024

Sponges, comprising over 9000 recorded species, represent one of the most primitive groups of metazoans. Given the importance of species distribution records and the identification of new species in scientific research, these endeavors play a crucial role in enhancing ecological insights, conserving biodiversity, facilitating a better understanding of the relationships between various groups of organisms, advancing our knowledge of evolution, and potentially expanding biomedical implications. In this study, we used basic morphological data, mitochondrial Cytochrome Oxidase I (COI) gene, and Internal Transcribed Spacer two (ITS2) regions to evaluate theTerpiossamples collected from four coastal sites along the northeastern Mediterranean Sea, covering a distance of approximately 450 km. For this purpose, 81 COI and 11 ITS2 records of the order Suberitida were mined from GenBank, and species delimitation analysis was performed using both the Automatic Barcode Gap Discovery method and the Poisson Tree Process (PTP), along with 11 samples from the present study. While we observed slight differences in spicule sizes, the overall morphology of all samples from our study was similar. Within the scope of this research, we report the first-ever presence record ofT. gelatinosusin the northeastern Mediterranean Sea. Furthermore, we document evidence pointing to the potential existence of cryptic speciation in the region.
De novo-designed minibinders expand the synthetic biology sensing repertoire
Authors: Weinberg Zara Y. , Soliman Sarah S. , Kim Matthew S. , Shah Devan H. , Chen Irene P. , Ott Melanie , Lim Wendell A. , El-Samad Hana
Published: January 2024

Synthetic and chimeric receptors capable of recognizing and responding to user-defined antigens have enabled “smart” therapeutics based on engineered cells. These cell engineering tools depend on antigen sensors which are most often derived from antibodies. Advances in thede novodesign of proteins have enabled the design of protein binders with the potential to target epitopes with unique properties and faster production timelines compared to antibodies. Building upon our previous work combining ade novo-designed minibinder of the Spike protein of SARS-CoV-2 with the synthetic receptor synNotch (SARSNotch), we investigated whether minibinders can be readily adapted to a diversity of cell engineering tools. We show that the Spike minibinder LCB1 easily generalizes to a next-generation proteolytic receptor SNIPR that performs similarly to our previously reported SARSNotch. LCB1-SNIPR successfully enables the detection of live SARS-CoV-2, an improvement over SARSNotch which can only detect cell-expressed Spike. To test the generalizability of minibinders to diverse applications, we tested LCB1 as an antigen sensor for a chimeric antigen receptor (CAR). LCB1-CAR enabled CD8+ T cells to cytotoxically target Spike-expressing cells. We further demonstrate that two other minibinders directed against the clinically relevant epidermal growth factor receptor are able to drive CAR-dependent cytotoxicity with efficacy similar to or better than an existing antibody-based CAR. Our findings suggest that minibinders represent a novel class of antigen sensors that have the potential to dramatically expand the sensing repertoire of cell engineering tools.
Large language models help facilitate the automated synthesis of information on potential pest controllers
Authors: Scheepens Daan , Millard Joseph , Farrell Maxwell , Newbold Tim
Published: January 2024

The body of ecological literature, which informs much of our knowledge of the global loss of biodiversity, has been experiencing rapid growth in recent decades. The increasing difficulty to synthesise this literature manually has simultaneously resulted in a growing demand for automated text mining methods. Within the domain of deep learning, large language models (LLMs) have been the subject of considerable attention in recent years by virtue of great leaps in progress and a wide range of potential applications, however, quantitative investigation into their potential in ecology has so far been lacking. In this work, we analyse the ability of GPT-4 to extract information about invertebrate pests and pest controllers from abstracts of a body of literature on biological pest control, using a bespoke, zero-shot prompt. Our results show that the performance of GPT-4 is highly competitive with other state-of-the-art tools used for taxonomic named entity recognition and geographic location extraction tasks. On a held-out test set, we show that species and geographic locations are extracted with F1-scores of 99.8% and 95.3%, respectively, and highlight that the model is able to distinguish very effectively between the primary roles of interest (predators, parasitoids and pests). Moreover, we demonstrate the ability of the model to effectively extract and predict taxonomic information across various taxonomic ranks, and to automatically correct spelling mistakes. However, we do report a small number of cases of fabricated information (hallucinations). As a result of the current lack of specialised, pre-trained ecological language models, general-purpose LLMs may provide a promising way forward in ecology. Combined with tailored prompt engineering, such models can be employed for a wide range of text mining tasks in ecology, with the potential to greatly reduce time spent on manual screening and labelling of the literature.
Clear effects of population and sex but not rearing temperature on stress tolerance in a temperate butterfly
Authors: Verspagen Nadja , DiLeo Michelle F. , Saastamoinen Marjo
Published: January 2024

As temperatures are rising globally, the survival of organisms depends on their tolerance of such rising temperatures as well as resistance to indirect effects such as resource shortage under these new conditions. Genetic background and phenotypic plasticity in the form of acclimation are known to affect stress resistance, but much about genetic variation in plasticity is still unknown, especially in insects other thanDrosophila. Here we aim to study the effect of population of origin, developmental temperature, and their interaction on stress tolerance (heat tolerance and starvation resistance). We test the beneficial acclimation hypothesis and how it is influenced by intraspecific differences. For this, we reared Glanville fritillary butterfly larvae originating from Finland and Spain at high and control temperatures, and measured their heat tolerance and starvation resistance. To assess potential costs of acclimation we also measured lifespan under control conditions. Neither adult heat tolerance nor starvation resistance were impacted by thermal conditions during development and thus we found no evidence for the beneficial acclimation hypothesis. Heat tolerance also did not differ between sex or population of origin. In contrast, we found interacting effects of population and sex on adult starvation resistance, with Spanish females outperforming other groups. Spanish females also had a longer lifespan under control conditions. Our study provides no evidence for the beneficial acclimation hypothesis but highlights the importance of population differences in stress tolerance.

SUMMARY STATEMENT

Despite their importance, the interacting effects of population of origin and developmental acclimation temperature on stress response have not often been studied together, especially in insects other thanDrosophila.
Stress Granule Protein TZF1 Enhances Salt Stress Tolerance by TargetingACA11mRNA for Degradation in Arabidopsis
Authors: He Siou-Luan , Li Bin , Zahurancik Walter J. , Arthur Henry C. , Sidharthan Vaishnavi , Gopalan Venkat , Wang Lei , Jang Jyan-Chyun
Published: January 2024

Tandem CCCH zinc finger (TZF) proteins play diverse roles in plant growth and stress response. Although as many as 11 TZF proteins have been identified inArabidopsis, little is known about the mechanism by which TZF proteins select and regulate the target mRNAs. Here, we report thatArabidopsisTZF1 is a bona-fide stress granule protein. Ectopic expression ofTZF1(TZF1 OE), but not an mRNA binding-defective mutant (TZF1H186YOE), enhances salt stress tolerance inArabidopsis. RNA-seq analyses of NaCl-treated plants revealed that the down-regulated genes inTZF1 OEplants are enriched for functions in salt and oxidative stress responses. Because many of these down-regulated mRNAs contain AU- and/or U-rich elements (AREs and/or UREs) in their 3’-UTRs, we hypothesized that TZF1—ARE/URE interaction might contribute to the observed gene expression changes. Results from RNA immunoprecipitation-quantitative PCR analysis, gel-shift, and mRNA half-life assays indicate that TZF1 binds and triggers degradation of theautoinhibited Ca2+-ATPase 11(ACA11) mRNA, encoding a tonoplast-localized calcium pump that extrudes calcium and dampens the signal transduction pathways necessary for salt stress tolerance. Furthermore, this salt stress-tolerance phenotype was recapitulated inaca11null mutants. Remarkably, a set of positive regulators for salt stress tolerance was upregulated inTZF1 OEplants. These includeNa+/H+Exchanger(NHX) family members known to contribute to Na+homeostasis and salinity stress tolerance. Collectively, we present a model in which TZF1 targetsACA11andACA4directly, and repressors ofNHXsand other negative regulators indirectly for mRNA degradation to enhance plant salt stress tolerance.
Assessing the role of pleiotropy in the evolution of animal color and behavior: a meta-analysis of experimental studies
Authors: Ruckman Sarah N. , Humphrey Eve A. , Muzzey Lily , Prantalou Ioanna , Pleasants Madison , Hughes Kimberly A.
Published: January 2024

Color varies in pattern and degree across the tree of life. In animals, genetic variation in color is hypothesized to have pleiotropic effects on a variety of behaviors, due to shared dependence on underlying biochemical pathways. Such pleiotropy can constrain the independent evolution of color and behavior. Although associations between color and behavior have been reported, this relationship has not yet been addressed across a broad taxonomic scale with a formal meta-analysis. We used a phylogenetic meta-analytic approach to examine the relationship between individual variation in aggressive behavior and variation in multiple colors. Seventy studies met our inclusion criteria (vertebrates = 66; invertebrates = 4). After accounting for phylogeny and correcting for publication bias, there was a positive association between measures of aggression and degree or area of coloration (mean = 0.274, 95% CI = (0.041, 0.481)). However, this positive association was not influenced by type of color or by several other variables that we tested. Because the data supports a positive association between aggression and degree or area of coloration, irrespective of whether color is melanin-based, carotenoid-based, or structural, we conclude that this pattern does not strongly support the melanin-pleiotropy hypothesis. The relationship was also unaffected by moderators accounting for individual condition, social rank, or age; thus, the results do not strongly support hypotheses that condition-dependence accounts for relationships between color and aggressive behavior. We propose that the moderate positive correlation between aggression and coloration across Animalia that we observed is underlain by genetic covariation between behavior and color traits that serve as badges of status.
Genome and tissue-specific transcriptome of the tropical milkweed (Asclepias curassavica)
Authors: Feng Honglin , Zhang Jing , Powell Adrian F. , Buttelmann Gretta L. , Yang Lily , Yan Ethan , Wang Fumin , Broyles Steven B. , Jander Georg , Strickler Susan R.
Published: January 2024

Tropical milkweed (Asclepias curassavica) serves as a host plant for monarch butterflies (Danaus plexippus) and other insect herbivores that can tolerate the abundant cardiac glycosides that are characteristic of this species. Cardiac glycosides, along with additional specialized metabolites, also contribute to the ethnobotanical uses ofA. curassavica. To facilitate further research on milkweed metabolism, we assembled the 197 Mbp genome of a fifth-generation inbred line ofA. curassavicainto 619 contigs, with an N50 of 10 Mbp. Scaffolding resulted in 98% of the assembly being anchored to 11 chromosomes, which are mostly colinear with the previously assembled common milkweed (A. syriaca) genome. Assembly completeness evaluations showed that 98% of the BUSCO gene set is present in theA. curassavicagenome assembly. The transcriptomes of six tissue types (young leaves, mature leaves, stems, flowers, buds, and roots), with and without defense elicitation by methyl jasmonate treatment, showed both tissue-specific gene expression and induced expression of genes that may be involved in cardiac glycoside biosynthesis. Expression of aCYP87Agene, the predicted first gene in the cardiac glycoside biosynthesis pathway, was observed only in the stems and roots and was induced by methyl jasmonate. Together, this genome sequence and transcriptome analysis provide important resources for further investigation of the ecological and medicinal uses ofA. curassavica.
AnNoBrainer, an Automated Annotation of Mouse Brain Images using Deep Learning
Authors: Peter Roman , Hrobar Petr , Navratil Josef , Vagenknecht Martin , Soukup Jindrich , Tsuji Keiko , Barrezueta Nestor X. , Stoll Anna C. , Gentzel Renee C. , Sugam Jonathan A. , Marcus Jacob , Bitton Danny A.
Published: January 2024

Annotation of multiple regions of interest across the whole mouse brain is an indispensable process for quantitative evaluation of a multitude of study endpoints in neuroscience digital pathology. Prior experience and domain expert knowledge are the key aspects for image annotation quality and consistency. At present, image annotation is often achieved manually by certified pathologists or trained technicians, limiting the total throughput of studies performed at neuroscience digital pathology labs. It may also mean that less rigorous, less time-consuming methods of histopathological assessment are employed by non-pathologists, especially for early discovery and preclinical studies. To address these limitations and to meet the growing demand for image analysis in a pharmaceutical setting, we developed AnNoBrainer, an open-source software tool that leverages deep learning, image registration, and standard cortical brain templates to automatically annotate individual brain regions on 2D pathology slides. Application of AnNoBrainer to a published set of pathology slides from transgenic mice models of synucleinopathy revealed comparable accuracy, increased reproducibility, and a significant reduction (∼50%) in time spent on brain annotation, quality control and labelling compared to trained scientists in pathology. Taken together, AnNoBrainer offers a rapid, accurate, and reproducible automated annotation of mouse brain images that largely meets the experts’ histopathological assessment standards (>85% of cases) and enables high-throughput image analysis workflows in digital pathology labs.
Antibiotics affect the pharmacokinetics of n-butylphthalidein vivoby altering the intestinal microbiota
Authors: Li Xiangchen , Guo Xiaoli , Liu Yixin , Ren Fefei , Li Shan , Yang Xiuling , Liu Jian , Zhang Zhiqing
Published: January 2024

Objective

N-butylphthalide (NBP) is a monomeric compound extracted from natural plant celery seeds, whether intestinal microbiota alteration can modify its pharmacokinetics is still unclear. The purpose of this study is to investigate the effect of intestinal microbiota alteration on the pharmacokinetics of NBP and its related mechanisms.

Methods

After treatment with antibiotics and probiotics, plasma NBP concentrations in SD rats were determined by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The effect of intestinal microbiota changes on NBP pharmacokinetics was compared. Intestinal microbiota changes after NBP treatment were analyzed by 16S rRNA sequencing. Expressions of CYP3A1 mRNA and protein in the liver and small intestine tissues under different intestinal flora conditions were determined by qRT-PCR and Western Blot. KEGG analysis was used to analyze the effect of intestinal microbiota changes on metabolic pathways.

Results

Compared to the control group, the values of Cmax, AUC0-8, AUC0-∞, t1/2in the antibiotic group increased by 56.1% (P<0.001), 56.4% (P<0.001), 53.2% (P<0.001), and 24.4% (P<0.05), respectively. In contrast, the CL and Tmaxvalues decreased by 57.1% (P<0.001) and 28.6% (P<0.05), respectively. Treatment with antibiotics could reduce the richness and diversity of the intestinal microbiota. CYP3A1 mRNA and protein expressions in the small intestine of the antibiotic group were 61.2% and 66.1% of those of the control group, respectively. CYP3A1 mRNA and protein expressions in the liver were 44.6% and 63.9% of those in the control group, respectively. There was no significant change in the probiotic group. KEGG analysis showed that multiple metabolic pathways were significantly down-regulated in the antibiotic group. Among them, the pathways of drug metabolism, bile acid biosynthesis and decomposition, and fatty acid synthesis and decomposition were related to NBP biological metabolism.

Conclusion

Antibiotic treatment could affect the intestinal microbiota, decrease CYP3A1 mRNA and protein expressions and increase NBP exposurein vivoby inhibiting pathways related to NBP metabolism.
pGpG-signaling regulates virulence and global transcriptomic targets inErwinia amylovora
Authors: Kharadi Roshni R. , Hsueh Brian Y. , Waters Christopher M. , Sundin George W.
Published: January 2024

Cyclic-di-GMP (c-di-GMP) is a critical bacterial second messenger that enables the physiological phase transition inErwinia amylovora, the phytopathogenic bacterium that causes fire blight disease. C-di-GMP generation is dependent on diguanylate cyclase enzymes while the degradation of c-di-GMP can occur through the action of phosphodiesterase (PDE) enzymes that contain an active EAL and/or a HD-GYP domain. The HD-GYP-type PDEs, which are absent inE. amylovora, can directly degrade c-di-GMP into two GMP molecules. PDEs that contain an active EAL domain, as found in all active PDEs inE. amylovora,degrade c-di-GMP into pGpG. The signaling function of pGpG is not fully understood in bacterial systems. A transcriptomic approach revealed that elevated levels of pGpG inE. amylovoraimpacted several genes involved in metabolic and regulatory functions including several type III secretion and extracellular appendage related genes. The heterologous overexpression of an EAL or HD-GYP-type PDE in different backgroundE. amylovorastrains with varying c-di-GMP levels revealed that in contrast to the generation of pGpG, the direct breakdown of c-di-GMP into GMP by the HD-GYP-type PDE led to an elevation in amylovoran production and biofilm formation despite a decrease in c-di-GMP levels. The breakdown of c-di-GMP into pGpG (as opposed to GTP) also led to a decrease in virulence in apple shoots. The expression ofhrpSwas significantly increased in response to the breakdown of c-di-GMP into pGpG. Further, our model suggests that a balance in the intracellular ratio of pGpG and c-di-GMP is essential for biofilm regulation inE. amylovora.

Importance

c-di-GMP is the keystone molecule for regulating the transition from motility to biofilm formation in most bacteria. Interestingly, there are two distinct enzymatic phosphodiesterase (PDE) domains, termed EAL and HD-GYP, that degrade c-di-GMP. EAL domains cleave one bond of the cyclic ring to generate pGpG while HD-GYP enzymes cleave c-di-GMP to two GMP molecules. A central question regarding c-di-GMP signaling is has whether or not pGpG itself functions as a signaling molecule. Here we demonstrate in the plant pathogenErwinia amylovorathat pGpG specifically regulates genes and contributes to biofilm formation and disease progression.
A Cytological F1 RNAi Screen for Defects inDrosophila melanogasterFemale Meiosis
Authors: Gilliland William D. , May Dennis P. , Bowen Amelia O. , Conger Kelly O. , Elrad Doreen , Marciniak Marcin , Mashburn Sarah A. , Presbitero Gabrielle , Welk Lucas F.
Published: January 2024

Genetic screens for recessive alleles induce mutations, make the mutated chromosomes homozygous, and then assay those homozygotes for the phenotype of interest. When screening for genes required for female meiosis, the phenotype of interest has typically been nondisjunction from chromosome segregation errors. As this requires that mutant females be viable and fertile, any mutants that are lethal or sterile when homozygous cannot be recovered by this approach. To overcome these limitations, our lab has screened the VALIUM22 collection produced by the Harvard TRiP Project, which contains RNAi constructs targeting genes known to be expressed in the germline in a vector optimized for germline expression. By driving RNAi with GAL4 under control of a germline-specific promoter (nanosormat-alpha4), we can test genes that would be lethal if knocked down in all cells, and by examining unfertilized metaphase-arrested mature oocytes, we can identify defects associated with genes whose knockdown results in sterility or causes other errors besides nondisjunction.

We screened this collection to identify genes that disrupt either of two phenotypes when knocked down: the ability of meiotic chromosomes to congress to a single mass at the end of prometaphase, and the sequestration of Mps1-GFP to ooplasmic filaments in response to hypoxia. After screening >1450 lines of the collection, we obtained multiple hits for both phenotypes, identified novel meiotic phenotypes for genes that had been previously characterized in other processes, and identified the first phenotypes to be associated with several previously uncharacterized genes.
Venturicidin A affects the mitochondrial membrane potential and induces kDNA loss inTrypanosoma brucei
Authors: Hauser Dennis , Kaiser Marcel , Mäser Pascal , Albisetti Anna
Published: January 2024

Neglected tropical diseases caused by trypanosomatid parasites have devastating health and economic consequences, especially in tropical areas. New drugs or new combination therapies to fight these parasites are urgently needed. Venturicidin A, a macrolide extracted fromStreptomyces, inhibits the ATP synthase complex of fungi and bacteria. However, its effect on trypanosomatids is not fully understood. In this study, we tested venturicidin A on a panel of trypanosomatid parasites using Alamar Blue assays and found it to be highly active againstTrypanosoma bruceiandLeishmania donovani, but much less so againstTrypanosoma evansi. Using fluorescence microscopy we observed a rapid loss of the mitochondrial membrane potential inT. bruceibloodstream forms upon venturicidin A treatment. Additionally, we report the loss of the mitochondrial DNA in approximately 40 to 50% of the treated parasites. We conclude that venturicidin A targets the ATP synthase ofT. brucei, and we suggest that this macrolide could be a candidate for antitrypanosomatid drug repurposing, drug combinations, or medicinal chemistry programs.
Fluorescence Lifetime Imaging for Quantification of Targeted Drug Delivery in Varying Tumor Microenvironments
Authors: Verma Amit , Pandey Vikas , Sherry Catherine , James Christopher , Matteson Kailie , Smith Jason T. , Rudkouskaya Alena , Intes Xavier , Barroso Margarida
Published: January 2024

Rationale

Trastuzumab (TZM) is a monoclonal antibody that targets the human epidermal growth factor receptor (HER2) and is clinically used for the treatment of HER2-positive breast tumors. However, the tumor microenvironment can limit the access of TZM to the HER2 targets across the whole tumor and thereby compromise TZM’s therapeutic efficacy. An imaging methodology that can non-invasively quantify the binding of TZM-HER2, which is required for therapeutic action, and distribution within tumors with varying tumor microenvironments is much needed.

Methods

We performed near-infrared (NIR) fluorescence lifetime (FLI) Forster Resonance Energy Transfer (FRET) to measure TZM-HER2 binding, usingin vitromicroscopy andin vivowidefield macroscopy, in HER2 overexpressing breast and ovarian cancer cells and tumor xenografts, respectively. Immunohistochemistry was used to validatein vivoimaging results.

Results

NIR FLI FRETin vitromicroscopy data show variations in intracellular distribution of bound TZM in HER2-positive breast AU565 and AU565 tumor-passaged XTM cell lines in comparison to SKOV-3 ovarian cancer cells. Macroscopy FLI (MFLI) FRETin vivoimaging data show that SKOV-3 tumors display reduced TZM binding compared to AU565 and XTM tumors, as validated byex vivoimmunohistochemistry. Moreover, AU565/XTM and SKOV-3 tumor xenografts display different amounts and distributions of TME components, such as collagen and vascularity. Therefore, these results suggest that SKOV-3 tumors are refractory to TZM delivery due to their disrupted vasculature and increased collagen content.

Conclusion

Our study demonstrates that FLI is a powerful analytical tool to monitor the delivery of antibody drug tumor both in cell cultures and in vivo live systems. Especially, MFLI FRET is a unique imaging modality that can directly quantify target engagement with potential to elucidate the role of the TME in drug delivery efficacy in intact live tumor xenografts.
Comparing DOACs with warfarin in AF patients with chronic kidney disease or valvular disease: A systematic review and meta-analysis
Authors: Liang Aileen , Wang Cathy , Iansavichene Alla E , Lazo-Langner Alejandro
Published: January 2024

Objective

To analyze the safety and efficacy of different direct oral anticoagulant agents (DOACs) compared to warfarin in patients with concomitant atrial fibrillation (AF) and valvular disease or concomitant AF and chronic kidney disease (CKD).

Methods

We conducted literature searches in MEDLINE, Embase, and EBM Reviews to examine randomized-controlled trials (RCTs) and non-RCTs that included the aforementioned patient populations treated with warfarin or DOAC (rivaroxaban, dabigatran, apixaban, or edoxaban) and assessed outcomes of bleeding, stroke, or systemic/arterial thromboembolism. Meta-analysis was performed for eligible studies using the Mantel-Haenszel method random-effects model.

Results

3,172 studies were screened and 154 studies were selected after two levels of screening. Meta-analysis showed that, in patients with concomitant AF and CKD, DOAC was associated with reduced bleeding in non-RCTs (OR 0.65, 95% Cl [0.49, 0.86], p=0.003), particularly in more severe CKD (eGFR < 60mL/min/1.73m2). Apixaban in particular was associated with reduced bleeding (OR 0.52, 95% Cl [0.44, 0.63], p<0.00001) and stroke incidence (OR 0.60, 95% Cl [0.41, 0.87], p=0.007). In patients with concomitant AF and valvular disease, DOAC was associated with reduced bleeding (OR 0.75, 95% CI [0.57, 0.97], p=0.03) and stroke incidence (OR 0.66, 95% CI [0.47, 0.93], p=0.02) in non-RCTs.

Conclusion

Our study studied populations that are typically excluded from large-scale anticoagulation studies and our findings suggest that DOACs may be superior to warfarin both in the prevention of thromboembolic event and in the reduction of bleeding risks in patients with concomitant CKD or valvular disease.
Somatic mutations in Alzheimer-associated tetraploid neurons
Authors: López-Sánchez Noelia , Rábano Alberto , Frade José M.
Published: January 2024

An early pathological process affecting the brain of Alzheimer’s disease (AD) is the reactivation of the cell cycle in neurons followed by somatic neuronal tetraploidization (NT). NT also increases with age, and ageing has been shown to correlate with the accumulation of DNA somatic mutations. In this study, we have evaluated the presence of somatic mutations including single nucleotide variants (SNVs) and indels in genomic DNA from tetraploid neurons obtained from the parietal cortex of AD patients, compared with diploid neurons from control individuals and AD patients. Here we show that, in contrast to somatic indels, the proportion of somatic SNVs (sSNVs) significantly increases in the exome of tetraploid neurons, having increased levels of T to C (A to G) transitions, a type of mutation that is associated with oxidative stress. This finding correlates with the over-representation of sSNVs in genes involved in oxidative stress response and DNA repair, suggesting that these alterations exacerbate oxidative DNA damage in tetraploid neurons. sSNVs affecting cancer-related (CR) genes showed a greater molecular pathogenicity score compared with those from a random sample of genes. We propose that neuronal tetraploidy is stochastically triggered through a CR mechanism in neurons whose DNA repair genes become mutated in an oxidative stress scenario. This mechanism likely participates in the etiology of AD.
Testing microbial biomining from asteroidal material onboard the International Space Station
Authors: Santomartino Rosa , Blanco Giovanny Rodriguez , Gudgeon Alfred , Hafner Jason , Stirpe Alessandro , Waterfall Martin , Cayzer Nicola , Pichevin Laetitia , Calder Gus , Birkenfeld Kyra R. , Waajen Annemiek C. , McLaughlin Scott , Mariani Alessandro , Balsamo Michele , Neri Gianluca , Eades Lorna J. , Cockell Charles S.
Published: January 2024

Expanding human space exploration beyond Earth’s orbit necessitates efficient technologies for self-sustainable acquisition of local resources to overcome unviable resupply missions from Earth. Potential source of materials are asteroids, some of which contain valuable metals, such as platinum group elements.

The BioAsteroid experiment, performed onboard the International Space Station, tested the use of microorganisms (bacteria and fungi) to carry out mining of useful elements from asteroidal material (L-chondrite) under microgravity, in support of a long-term human presence in space. The fungusPenicillium simplicissimum, enhanced the mean release of palladium, platinum and other elements from the meteorite material in microgravity, compared to non-biological leaching. However, there was large variability in the results. For many elements, non-biological leaching under microgravity was enhanced compared to terrestrial gravity, while bioleaching was unaffected. Metabolomics results revealed clear patterns that highlight the influence of space conditions on the microbial metabolism, particularly forP. simplicissimum. We identified the presence of carboxylic acids, and molecules of potential biomining and pharmaceutical interest, enhanced in microgravity.

These results show a non-trivial effect of microgravity on bioleaching, highlighting the requirement of an optimal combination of microorganism(s), rock substrate, and conditions for successful biomining, both in space and Earth.
Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems
Authors: Giannantoni Leonardo , Bardini Roberta , Savino Alessandro , Di Carlo Stefano
Published: January 2024

Background

The Biology System Description Language (BiSDL) is an accessible, easy-to-use computational language for multicellular synthetic biology. It allows synthetic biologists to represent spatiality and multi-level cellular dynamics inherent to multicellular designs, filling a gap in the state of the art. Developed for designing and simulating spatial, multicellular synthetic biological systems, BiSDL integrates high-level conceptual design with detailed low-level modeling, fostering collaboration in the Design-Build-Test-Learn cycle. BiSDL descriptions directly compile into Nets-Within-Nets (NWNs) models, offering a unique approach to spatial and hierarchical modeling in biological systems.

Results

BiSDL’s effectiveness is showcased through three case studies on complex multicellular systems: a bacterial consortium, a synthetic morphogen system and a conjugative plasmid transfer process. These studies highlight the BiSDL proficiency in representing spatial interactions and multi-level cellular dynamics. The language facilitates the compilation of conceptual designs into detailed, simulatable models, leveraging the NWNs formalism. This enables intuitive modeling of complex biological systems, making advanced computational tools more accessible to a broader range of researchers.

Conclusions

BiSDL represents a significant step forward in computational languages for synthetic biology, providing a sophisticated yet user-friendly tool for designing and simulating complex biological systems with an emphasis on spatiality and cellular dynamics. Its introduction has the potential to transform research and development in synthetic biology, allowing for deeper insights and novel applications in understanding and manipulating multicellular systems.
Death Incidents Following Transcatheter Edge-to-Edge Repair (TEER) With the MitraClip Device: Analysis of 10-years Post-marketing Death Reports from the Manufacturer and User Facility Device Experience (MAUDE) Registry
Authors: Sun Xing-he , Zhao Yi-fei , Li Yan
Published: January 2024

Background

The MitraClip device (Abbott), an FDA-approved transcatheter apparatus, is employed for the management of mitral regurgitation (MR) among patients deemed at high risk for surgical interventions. We analyzed reports in the FDA MAUDE database to evaluate the safety trend in fatal complications associated with MitraClip implantation in the last decade.

Methods

We searched the publicly accessible Manufacturer and User Facility Device Experience (MAUDE) database for reports of deaths and injuries associated with MitraClip implantation from October 2013 to September 2023. Duplicate reports were excluded. The Cochran-Armitage test was used to analyze the trend in proportion of fatal events.

Results

In the 10 year period after FDA approval, a total of 927 death reports and 9211 injury reports were recorded by the MAUDE database. 592 death reports were included for analysis after excluding duplicates and reports from other sources. The most frequently reported complications were MR (26.69%), tissue damage (24.16%) and hypotension (22.13% ). The most common device-related problems were incomplete coaptation (14.70%), difficult to remove (6.42%), and failure to adhere or bond/positioning failure(4.90%). Most deaths (76.94%) occurred within one year of implantation. The proportion of reported fatal events showed a significant declining trend from 15.9% in 2014-2015 to 3.5% in 2020-2021 (p<0.0001).

Conclusions

Analysis of the MAUDE database suggests a decline in reported fatal events associated with MitraClip implantation over time, which may reflect increasing experience with the device. However, passive reporting has limitations including underreporting and incomplete data. Further studies are needed to better characterize the safety profile and complication rates of MitraClip implantation in real-world practice.
Transcription of a centromere-enriched retroelement and local retention of its RNA are significant features of the CENP-A chromatin landscape
Authors: Santinello B , Sun R , Amjad A , Hoyt SJ , Ouyang L , Courret C , Drennan R , Leo L , Larracuente AM , Core L , O’Neill RJ , Mellone BG
Published: January 2024

Centromeres depend on chromatin containing the conserved histone H3 variant CENP-A for function and inheritance, while the role of centromeric DNA repeats remains unclear. Retroelements are prevalent at centromeres across taxa and represent a potential mechanism for promoting transcription to aid in CENP-A incorporation or for generating RNA transcripts to maintain centromere integrity. Here, we probe into the transcription and RNA localization of the centromere-enriched retroelementG2/Jockey-3(hereafter referred to asJockey-3) inDrosophila melanogaster, currently the onlyin vivomodel with assembled centromeres. We find thatJockey-3is a major component of the centromeric transcriptome and produces RNAs that localize to centromeres in metaphase. Leveraging the polymorphism ofJockey-3and ade novocentromere system, we show that these RNAs remain associated with their cognate DNA sequences incis, suggesting they are unlikely to perform a sequence-specific function at all centromeres. We show thatJockey-3transcription is positively correlated with the presence of CENP-A, and that recentJockey-3transposition events have occurred preferentially at CENP-A-containing chromatin. We propose thatJockey-3contributes to the epigenetic maintenance of centromeres by promoting chromatin transcription, while inserting preferentially within these regions, selfishly ensuring its continued expression and transmission. Given the conservation of retroelements as centromere components through evolution, our findings have broad implications in understanding this association in other species.
Multi-condensate state as a functional strategy to optimize the cell signaling output
Authors: Chattaraj Aniruddha , Shakhnovich Eugene I
Published: January 2024

The existence of multiple biomolecular condensates inside living cells is a peculiar phenomenon not compatible with the predictions of equilibrium statistical mechanics. In this work, we address the problem of multiple condensates state (MCS) from a functional perspective. We combined Langevin dynamics, reaction-diffusion simulation, and dynamical systems theory to demonstrate that MCS can indeed be a function optimization strategy. Using Arp2/3 mediated actin nucleation pathway as an example, we show that actin polymerization is maximum at an optimal number of condensates. For a fixed amount of Arp2/3, MCS produces a greater response compared to its single condensate counterpart. Our analysis reveals the functional significance of the condensate size distribution which can be mapped to the recent experimental findings. Given the spatial heterogeneity within condensates and non-linear nature of intracellular networks, we envision MCS to be a generic functional solution, so that structures of network motifs may have evolved to accommodate such configurations.
Deciphering the co-evolutionary dynamics of L2 β-lactamases via Deep learning
Authors: Zhu Yu , Gu Jing , Zhao Zhuoran , Chan A W Edith , Mojica Maria F. , Hujer Andrea M. , Bonomo Robert A. , Haider Shozeb
Published: January 2024

L2 β-lactamases, a serine-based class A β-lactamases expressed byStenotrophomonas maltophiliaplays a pivotal role in antimicrobial resistance. However, limited studies have been conducted on these important enzymes. To understand the co-evolutionary dynamics of L2 β-lactamase, innovative computational methodologies, including adaptive sampling molecular dynamics simulations, and deep learning methods (convolutional variational autoencoders and BindSiteS-CNN) explored conformational changes and correlations within the L2 β-lactamase family together with other representative class A enzymes including SME-1 and KPC-2. This work also investigated the potential role of hydrophobic nodes and binding site residues in facilitating the functional mechanisms. The convergence of analytical approaches utilized in this effort yielded comprehensive insights into the dynamic behaviour of the β-lactamases, specifically from an evolutionary standpoint. In addition, this analysis presents a promising approach for understanding how the class A β-lactamases evolve in response to environmental pressure and establishes a theoretical foundation for forthcoming endeavours in drug development aimed at combating antimicrobial resistance.

Synopsis

Deep learning is used to reveal the dynamic co-evolutionary patterns of L2 β-lactamases.

Analysis of hydrophobic nodes and binding site residues provides a detailed understanding of both local and global dynamic evolution, which explain the functional divergences.

The employment of two distinct deep learning models, the Convolutional Variational Autoencoder (CVAE) and BindSiteS-CNN, facilitates the investigation of conformational shifts, thereby depicting the dynamic evolution of L2 β-lactamases.

The effectiveness of CVAE and BindSiteS-CNN in dynamic classification is corroborated with selected features.

Abstract Figure
Safety and efficacy study of CRISPR/Cas9 treatment of sickle cell disease in clinically relevant conditions highlights disease-specific response
Authors: Frati Giacomo , Brusson Megane , Sartre Gilles , MLAYAH Bochra , FELIX Tristan , Chalumeau Anne , Antoniou Panagiotis , Hardouin Giulia , Concordet Jean-Paul , Romano Oriana , Turchiano Giandomenico , Miccio Annarita
Published: January 2024

Reactivation of fetal hemoglobin (HbF) expression through clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-mediated disruption of regulatory elements involved in γ-globin gene repression is a promising gene therapy strategy for the treatment of sickle cell disease (SCD). However, preclinical studies aimed at optimizing the genome editing process and evaluating the safety of the editing strategy are necessary to translate this approach to the clinics. This is particularly relevant in the context of SCD, a disease characterized by inflammation, which can affect hematopoietic stem and progenitor cells (HSPCs), the target cell population in gene therapy approaches for hematopoietic disorders. Here, we describe a genome editing strategy leading to therapeutically relevant reactivation of HbF expression by targeting the binding sites (BSs) for the leukemia/lymphoma related factor (LRF) transcriptional repressor in the HBG1 and HBG2 γ-globin promoters. Electroporation of Cas9 ribonucleoprotein and single guide RNA (sgRNA) targeting the HBG promoters in healthy donor (HD) and patient-derived HSPCs resulted in a high frequency of LRF BS disruption and potent HbF synthesis in their erythroid progeny differentiated in vitro and ex vivo after transplantation into immunodeficient mice. LRF BS disruption did not impair SCD and HD HSPC engraftment and differentiation, but was more efficient in SCD than in HD cells. However, SCD HSPCs showed a reduced engraftment and a myeloid bias compared to HD cells. Importantly, in primary HSPCs, we detected off-target activity and the intra- and inter-chromosomal rearrangements between on- and off-target sites, which were more pronounced in SCD samples (likely because of the higher overall editing efficiency), but did not impact the target gene expression. Off-target activity was observed in vitro and in vivo, thus indicating that it does not impair engraftment and differentiation of both SCD and HD HSPCs. Finally, transcriptomic analyses showed that the genome editing procedure results in the upregulation of genes involved in DNA damage and inflammatory responses in both HD and SCD samples, although gene dysregulation was more evident in SCD HSPCs. Overall, this study provides evidences of feasibility, efficacy and safety for a genome editing strategy based on HbF reactivation and highlights the need of performing safety studies, when possible, in clinically relevant conditions, i.e., in patient-derived HSPCs.