bluuebunny/crossref_metadata_2025 huggingface dataset:
Differential gene expression and mitonuclear incompatibilities in fast- and slow-developing inter-population Tigriopus californicus hybrids
Authors: Healy Timothy M. , Burton Ronald S.
Published: September 2022

Mitochondrial functions are intimately reliant on proteins and RNAs encoded in both the nuclear and mitochondrial genomes, leading to inter-genomic coevolution within taxa. Hybridization can break apart coevolved mitonuclear genotypes, resulting in decreased mitochondrial performance and reduced fitness. This hybrid breakdown is an important component of outbreeding depression and early-stage reproductive isolation.

However, the mechanisms contributing to mitonuclear interactions remain poorly resolved. Here we scored variation in developmental rate (a proxy for fitness) among reciprocal F2 inter-population hybrids of the intertidal copepod Tigriopus californicus, and used RNA sequencing to assess differences in gene expression between fast- and slow-developing hybrids. In total, differences in expression associated with developmental rate were detected for 2,925 genes, whereas only 135 genes were differentially expressed as a result of differences in mitochondrial genotype. Up-regulated expression in fast developers was enriched for genes involved in chitin-based cuticle development, oxidation-reduction processes, hydrogen peroxide catabolic processes and mitochondrial respiratory chain complex I. In contrast, up-regulation in slow developers was enriched for DNA replication, cell division, DNA damage and DNA repair. Eighty-four nuclear-encoded mitochondrial genes were differentially expressed between fast- and slow-developing copepods, including twelve subunits of the electron transport system (ETS) which all had higher expression in fast developers than in slow developers. Nine of these genes were subunits of ETS complex I. Our results emphasize the major roles that mitonuclear interactions within the ETS, particularly in complex I, play in hybrid breakdown, and resolve strong candidate genes for involvement in mitonuclear interactions.
Mapping global land sharing-sparing patterns between human and wildlife
Authors: Zhang Chengcheng , Wang Yihong , Pan Shengkai , Yang Biao , Zhan Xiangjiang , Chang Jiang , Li Junsheng , Dai Qiang
Published: September 2022

Understanding the global patterns of land sharing-sparing between humans and wildlife is essential for pragmatic conservation implementation, yet analytical foundations and indicator-based assessments are still lacking. By integrating distributions of 30,664 terrestrial vertebrates and human pressures, we provide a series of spatial explicit Human-Nature Indices (HNIs) before classifying the global lands into four categories. We found that the Co-occurring (C) regions, where lands are shared by humans and wildlife, are not insignificant (16.91% of global land). For land-sparing, the Diversity-intact (D) and the Anthropic (A) regions account for 45.64% and 1.41% of the land, respectively. The patterns of HNIs, varying considerably among taxonomic groups, are determined mainly by the expansion of human-dominated land use. Land sharing and sparing could work as complementary strategies to support biodiversity and human development toward ambitious and pragmatic 30 by 30 goals. Our results highlight that those regions should adopt different conservation strategies according to their sharing-sparing patterns and distribution of protected areas.
Orientation-locked DNA origami for stable trapping of small proteins in the NEOtrap
Authors: Wen Chenyu , Bertosin Eva , Shi Xin , Dekker Cees , Schmid Sonja
Published: September 2022

Nanopores are versatile single-molecule sensors that offer a simple label-free readout with great sensitivity. We recently introduced the Nanopore Electro-Osmotic trap (NEOtrap) which can trap and sense single unmodified proteins for long times. The trapping is achieved by the electro-osmotic flow (EOF) generated from a DNA-origami sphere docked onto the pore, but thermal fluctuations of the origami limited the trapping of small proteins. Here, we use site-specific cholesterol functionalization of the origami sphere to firmly link it to the lipid-coated nanopore. We can lock the origami in either a vertical or horizontal orientation which strongly modulates the EOF. The optimized EOF greatly enhances the trapping capacity, yielding reduced noise, reduced measurement heterogeneity, an increased capture rate, and 100-fold extended observation times. We demonstrate the trapping of a variety of single proteins, including small ones down to a molecular mass of 14 kDa. The cholesterol functionalization significantly expands the application range of the NEOtrap technology.
An Immune Cell Recirculation-Enabled Microfluidic Array to Study Dynamic Immunotherapeutic Activity in Recapitulated Tumor Microenvironment
Authors: Chi Chun-Wei , Lao Yeh-Hsing , Ahmed AH Rezwanuddin , He Siyu , Merghoub Taha , Leong Kam W. , Wang Sihong
Published: September 2022

The efficacy of immunotherapeutic treatment protocols to enable immune cell mediated treatment of cancer is significantly modulated in the presence of tumor microenvironment (TME) which is a key factor in providing both a physical barrier and immunosuppressive stimuli. Herein, we developed a recirculating, high-throughput microfluidic cell array to capture these crucial players – cytotoxic T cells in circulation, endothelium, and tumor stroma. The system consisted of a three-layered cell array spatially emulating TME, with T cell circulation sustained via fluidic recirculating circuits. This allowed us to study the dynamic TME/circulation system and cancer cell response thereof. The system further revealed that tumor endothelium exhibited a hindrance to T cell infiltration into the breast cancer tumor compartment, which was alleviated when treated with anti-human PD-L1 antibody. The other key stromal component, cancer associated fibroblasts, further attenuated T cell infiltration, and led to reduced apoptosis activity in cancer cells. These results confirm the capability of our tumor-on-a-chip system to recapitulate some key immune cell interactions with the reconstructed TME, along with demon-strating as the feasibility of using this system for high-throughput cancer immunotherapeutic screening.
Body mass change over winter is consistently sex-specific across roe deer (Capreolus capreolus) populations
Authors: Hewison A.J.M. , Bonnot N.C. , Gaillard J.M. , Kjellander P. , Lemaitre J.F. , Morellet N. , Pellerin M.
Published: September 2022

In most polygynous vertebrates, males must allocate energy to growing secondary sexual characteristics, such as ornaments or weapons, that they require to attract and defend potential mates, impacting body condition and potentially entailing fitness costs.

We investigated sex differences in over winter body mass change across five intensively monitored populations of roe deer (Capreolus capreolus) with markedly contrasting environmental conditions. At winter onset, males weighed, on average, 8.4% (from 4.7% in the most northerly population to 11.6% in the most southerly one) more than females. However, across all populations, males fared worse over the winter than females, losing more (Sweden) or gaining less (France) mass, so that sexual mass dimorphism was virtually absent prior to the onset of spring.

Our findings reveal that the direction of over-winter change in mass of roe deer depends on winter severity, but that males are consistently more sensitive to this environmental constraint than females. As a result of this sex-specific change in body mass, sexual mass dimorphism is lowest at the onset of the territorial season. We suggest that allocation to antler growth and territory establishment drives this pattern, providing a likely explanation to account for the lower rates of male adult survival that are consistently reported in this weakly dimorphic species.
Dating the origin and spread of specialization on human hosts in Aedes aegypti mosquitoes
Authors: Rose Noah H. , Badolo Athanase , Sylla Massamba , Akorli Jewelna , Otoo Sampson , Gloria-Soria Andrea , Powell Jeffrey R. , White Bradley J. , Crawford Jacob E. , McBride Carolyn S.
Published: September 2022

The globally invasive mosquito subspecies Aedes aegypti aegypti is a highly effective vector of human arboviruses because it specializes in biting humans and breeding in human habitats. Recent work suggests that specialization first arose as an adaptation to long, hot dry seasons in the West African Sahel, where Ae. aegypti is forced to rely on human-stored water for breeding. However, rainfall patterns in this region have changed dramatically over the past 10-20 thousand years, and we do not yet know exactly when specialization occurred. Here we use whole-genome cross-coalescent analysis to date the emergence of human specialist populations in the Sahel and thus further probe the climate hypothesis. Importantly, we take advantage of the known migration of human-specialist populations out of Africa during the Atlantic Slave Trade to calibrate the coalescent clock and thus obtain a more precise estimate of the older evolutionary event than would otherwise be possible. We find that human-specialist mosquitoes diverged rapidly from ecological generalists approximately 5,000 years ago, which corresponds to the end of the African Humid Period—a time when the Sahara dried and water stored by humans became a uniquely stable, aquatic niche in the Sahel. We also use population genomic analyses to date a previously observed influx of human-specialist alleles into major West African cities, where mosquitoes tend to be more attracted to humans than in nearby rural populations regardless of climate. In this case, the characteristic length of tracts of human-specialist ancestry present on a generalist genetic background in Kumasi, Ghana and Ouagadougou, Burkina Faso suggests the change in behavior occurred during rapid urbanization over the last 20-40 years. Taken together, we show that the timing and ecological context of two previously observed shifts towards human biting in Ae. aegypti differ; climate was likely the original driver, but urbanization has become increasingly important in recent decades. Understanding the changing relationship between mosquitoes and humans over time is critical for predicting and managing burdens of mosquito-borne disease.
Inorganic phosphate content does not affect oviposition preference in the invasive pestDrosophila suzukii
Authors: Olazcuaga Laure , Guilhot Robin , Claret Jean-Loup , Rode Nicolas O.
Published: September 2022

The broad variation in host use among polyphagous insects is well documented but still poorly understood. In numerous pest insects, the proximate mechanisms responsible for variation in oviposition preference among host plants remain to be elucidated. The invasive crop pest,Drosophila suzukii, attacks a wide range of host fruits. Females prefer ovipositing on particular fruit media (blackberry, cherry, blackcurrant) that are rich in phosphorus. As phosphorus is known to be involved in female reproduction in insect species such as Drosophila, it could drive oviposition preference inD. suzukii. Phosphorus is either present as inorganic or organic phosphate in fruits. As the absolute content in macromolecules associated with phosphate in fruits (i.e. proteins and carbohydrates) do not affect oviposition inD. suzukii, we tested for the effect of inorganic phosphate on oviposition preference. We measured the egg-laying preferences ofD. suzukiiin a choice environment containing 12 artificial media with increasing content in inorganic phosphate (monopotassium dihydrogen phosphate). In our assay,D. suzukiifemales did not prefer ovipositing in media with high inorganic phosphate content compared to media with lower inorganic phosphate content. As a confirmation, we verified the previous result of a higher female preference for media made of phosphorus-rich fruits (blackberry, cherry, blackcurrant). The higher preference for phosphorus-rich fruits could be driven by macromolecules containing phosphorus (e.g. phospholipids) or by the presence of one or more molecules that do not contain phosphorus, but that happen to be correlated to fruit phosphorus content. Studying the proximate mechanisms driving host use will ultimately help improve the management ofD. suzukiiand other crop pests.
The influence of the social environment on larval development and resulting caste inBombus impatiens
Authors: Barie Katherine , Amsalem Etya
Published: September 2022

The ability of a single genome to express multiple phenotypes is key to understanding social evolution, where individuals with different morphologies perform different tasks. In social insects, phenotypes are typically determined during larval development and depend on the social environment. Here, we used the bumble beeBombus impatiensto examine the social regulation of body size variation and caste by manipulating the identity (queen/worker) and the number of caretakers tending for the brood. Eggs of females and males were kept in cages with (1) a single queen; (2) a single worker; (3) three workers; or (4) ten workers. We measured larval weight, developmental length, and the resulting caste (in females) throughout the brood development of >2000 individuals. We found differences in larval mass when reared by varying number of workers, but not when reared by a single worker compared to a queen. Additionally, in contrast with previous findings inB. terrestris, none of the female eggs reared by workers developed into gynes (new queens), indicating that the mechanisms regulating caste determination inB. impatiensis not solely dependent on the queen presence as inB. terrestris. Adult males were slightly larger than workers and developed for a longer period in the presence of the queen. Overall, we suggest that body size inB. impatiensis determined by the number of caretakers and is likely mediated by the amount of provision. The hypothesis that the queen’s presence manipulates female caste was not supported by our data.
Effects of ancient anthropogenic clam gardens on the growth, survival, and transcriptome of Pacific littleneck clams (Leukoma staminea)
Authors: Raap Monique R. , Gurney-Smith Helen J. , Dudas Sarah E. , Pearce Christopher M. , Leong Jong S. , Sutherland Ben J.G. , Koop Ben F.
Published: September 2022

Clam gardens traditionally established and maintained by coastal Indigenous Peoples of northwest North America are habitat modifications that enhance intertidal clam productivity and therefore provide secure and reliable local food resources. In this study, transcriptomic and phenotypic responses of Pacific littleneck clams (Leukoma staminea) were investigated in relation to transplantation to either clam gardens or unmodified clam beaches and growth for 16 weeks. Sediment characteristics (e.g., grain-size, carbonate, and organic content) were also evaluated and considered in the response. Large differences in phenotypic and abiotic characteristics were observed among beaches but did not differ based on unmaintained clam garden presence. Ade novotranscriptome forL. stamineacontaining 52,000 putative transcripts was assembled and used to identify differential expression in response to the clam gardens. This identified a relatively small effect, but found two transcripts that were differentially expressed in both the gill and digestive gland tissues. In addition, differential expression along survival gradients, as well a tissue-specific expression analysis provide insight into the characteristics of the transcriptome and its ecological associations of this non-model organism. Across the beaches, abiotic characteristics with negative effects on growth and/or survival included small rocks, very fine sand, silt, carbonate, and organic content, whereas positive effects were observed from coarse sand, sand and fine sand. In conclusion, here it was found that localized environmental factors are likely to have a greater influence on Pacific littleneck clam physiology, growth, and survival than the presence or absence of unmaintained clam gardens.
Rhythmic Modulation of Visual Discrimination is Dependent on Individuals’ Spontaneous Motor Tempo
Authors: Snapiri Leah , Kaplan Yael , Shalev Nir , Landau Ayelet N.
Published: September 2022

Rhythmic structure in our daily experience originates from various sources. It is generated endogenously and observed in spontaneous fluctuations in behaviour and performance. It can also arise exogenously from everyday stimuli, such as speech, motion and music. Here we examined how individual differences in spontaneous motor rhythms affect the tendency to use external rhythmic structure to guide perception. To measure individual differences in spontaneous rhythms of performance we utilized a spontaneous tapping task. To measure individual differences in perceptual rhythmic modulation we designed a visual discrimination task in which targets can appear either in-phase or out-of-phase with a preceding rhythmic stream of visual stimuli. We manipulated the tempo of the visual stream over different experimental blocks (0.77 Hz, 1.4 Hz, 2 Hz). We found that visual rhythmic stimulation modulates discrimination performance. The modulation was dependent on the tempo of stimulation, with maximal perceptual benefits for the slowest tempo of stimulation (0.77 Hz). Most importantly, the strength of modulation was also affected by individuals’ spontaneous motor tempo. Specifically, individuals with slower spontaneous tempi showed greater rhythmic modulation compared to individuals with faster spontaneous tempi. This discovery suggests that different tempi affect the cognitive system with varying levels of efficiency, and that self-generated rhythms impact our ability to utilize rhythmic structure in the environment for guiding perception and performance.
Root System Architecture and Environmental Flux Analysis in Mature Crops using 3D Root Mesocosms
Authors: Dowd Tyler G. , Li Mao , Bagnall G. Cody , Johnston Andrea , Topp Christopher N.
Published: September 2022

Current methods of root sampling typically only obtain small or incomplete sections of root systems and do not capture their true complexity. To facilitate the visualization and analysis of full-sized plant root systems in 3-dimensions, we developed customized mesocosm growth containers. While highly scalable, the design presented here uses an internal volume of 45 ft3 (1.27 m3), suitable for large crop and bioenergy grass root systems to grow largely unconstrained. Furthermore, they allow for the excavation and preservation of 3-dimensional RSA, and facilitate the collection of time-resolved subterranean environmental data. Sensor arrays monitoring matric potential, temperature and CO2 levels are buried in a grid formation at various depths to assess environmental fluxes at regular intervals. Methods of 3D data visualization of fluxes were developed to allow for comparison with root system architectural traits. Following harvest, the recovered root system can be digitally reconstructed in 3D through photogrammetry, which is an inexpensive method requiring only an appropriate studio space and a digital camera. We developed a pipeline to extract features from the 3D point clouds, or from derived skeletons that include point cloud voxel number as a proxy for biomass, total root system length, volume, depth, convex hull volume and solidity as a function of depth. Ground-truthing these features with biomass measurements from manually dissected root systems showed a high correlation. We evaluated switchgrass, maize, and sorghum root systems to highlight the capability for species wide comparisons. We focused on two switchgrass ecotypes, upland (VS16) and lowland (WBC3), in identical environments to demonstrate widely different root system architectures that may be indicative of core differences in their rhizoeconomic foraging strategies. Finally, we imposed a strong physiological water stress and manipulated the growth medium to demonstrate whole root system plasticity in response to environmental stimuli. Hence, these new “3D Root Mesocosms” and accompanying computational analysis provides a new paradigm for study of mature crop systems and the environmental fluxes that shape them.
Comprehensive Analysis of Regenerative and Transformed Liver Reveals Distinct, Early Metabolic Alterations in Cancer
Authors: McLaughlin Daniel J. , Mir Hannan , Nam Minwoo , Possemato Richard
Published: September 2022

Alterations in cellular metabolism represent an important response to proliferative signals in both normal and transformed tissues. The benign proliferative process of liver regeneration after partial hepatectomy offers insight into homeostatic mechanisms to control liver mass, which are disrupted in liver disease induced by viral factors, alcohol, or associated with obesity. Moreover, successful targeting of cancer depends on the identification of genes and pathways that are selectively activated in the transformed state. Here, we present a differential transcriptomic and metabolomic analysis of benign proliferative and transformed liver, including associated plasma metabolite and lipid species. Using partial hepatectomy-induced liver regeneration and diethylnitrosamine (DEN) induced carcinogenesis, we identify and analyze alterations specific to multiple regenerative and transformed tissue states. Transcriptomics and LC/MS based metabolite profiling reveal fatty acid import and storage are specifically rewired during liver regeneration in a time dependent manner, a phenomenon not observed in liver tumors. In contrast, liver tumors exhibit preferential activation of numerous metabolic pathways, including glycolysis, serine biosynthesis, and polyamine metabolism. Alterations in serine metabolism occur at the earliest detectable stages in tumorigenesis and promote survival upon serine restriction. These data demonstrate that transformation-induced alterations in metabolism are distinct from those observed in normal regenerative cell division, which may be used to identify transformation-specific liabilities.
Enhancing adoptive T cell therapy with synergistic host immune engagement promotes long-term protection against solid tumors
Authors: Adu-Berchie Kwasi , Brockman Joshua M. , Liu Yutong , Zhang David K.Y. , Najibi Alexander J. , Stafford Alexander , Sobral Miguel C. , Binenbaum Yoav , Dellacherie Maxence O. , Mooney David J.
Published: September 2022

Adoptive T cell therapy provides the T cell pool needed for immediate tumor debulking, but the infused T cells generally have a narrow repertoire for antigen recognition and limited ability for long-term protection. Here, we present a biomaterial platform that enhances adoptive T cell therapy by synergistically engaging the host immune system via in-situ antigen-free vaccination. T cells alone loaded into these localized cell depots provided significantly better control of subcutaneous B16-F10 tumors than T cells delivered through direct peritumoral injection or intravenous infusion. The anti-tumor response was significantly enhanced when T cell delivery was combined with biomaterial-driven accumulation and activation of host immune cells, as this prolonged the activation state of the delivered T cells, minimized host T cell exhaustion, and enabled long-term tumor control. This integrated approach provides both immediate tumor debulking and long-term protection against solid tumors, including against tumor antigen escape.
Max is likely not at the Drosophila histone locus
Authors: Xie Mellisa , Comstra Skye , Schmidt Casey , Hodkinson Lauren , Rieder Leila E.
Published: September 2022

The histone locus body (HLB) is a conserved nuclear body that regulates histone mRNA production in metazoans. While some HLB components are known, there are likely uncharacterized factors that target the histone locus. We identified the Drosophila melanogaster protein Max, which interacts with known HLB member Myc, as an HLB candidate. We mapped Max ChIP-seq and ChIP-nexus datasets, which revealed encouraging signal over the histone gene array. However, we discovered that Max does not colocalize with HLB components on polytene chromosomes. Therefore, we conclude that Max is likely not at the D. melanogaster histone locus.
Microbial glutamate metabolism predicts intravenous cocaine self-administration in Diversity Outbred mice
Authors: Tran Thi Dong Binh , Nguyen Hoan , Sodergren Erica ,   Center for Systems Neurogenetics of Addiction, Dickson Price E , Wright Susan N , Philip Vivek M , Weinstock George M. , Chesler Elissa J. , Zhou Yanjiao , Bubier Jason A.
Published: September 2022

The gut microbiome is thought to play a critical role in the onset and development of psychiatric disorders, including depression and substance use disorder (SUD). To test the hypothesis that the microbiome affects addiction predisposing behaviors and cocaine intravenous self-administration (IVSA) and to identify specific microbes involved in the relationship, we performed 16S rRNA gene sequencing on feces from 228 diversity outbred mice. Twelve open field measures, two light-dark assay measures, one hole board and novelty place preference measure significantly differed between mice that acquired cocaine IVSA (ACQ) and those that failed to acquire IVSA (FACQ). We found that ACQ mice are more active and exploratory and display decreased fear than FACQ mice. The microbial abundances that differentiated ACQ from FACQ mice were an increased abundance ofBarnesiella, Ruminococcus, andRobinsoniellaand decreasedClostridium IVin ACQ mice. There was a sex-specific correlation between ACQ and microbial abundance, a reducedLactobacillusabundance in ACQ male mice, and a decreasedBlautiaabundance in female ACQ mice. The abundance ofRobinsoniellawas correlated, andClostridium IVinversely correlated with the number of doses of cocaine self-administered during acquisition. Functional analysis of the microbiome composition of a subset of mice suggested that gut-brain modules encoding glutamate metabolism genes are associated with the propensity to self-administer cocaine. These findings establish associations between the microbiome composition and glutamate metabolic potential and the ability to acquire cocaine IVSA thus indicating the potential translational impact of targeting the gut microbiome or microbial metabolites for treatment of SUD.

HIGHLIGHTS

Correlational analysis of novelty behaviors to IVSA acquisition shows that mice that acquire cocaine IVSA are more active and exploratory and have decreased fear than those that failed-to-acquire IVSA.

The gut microbiome profiling of 228 diversity outbred mice indicates the relative abundances ofBarnesiella, Ruminococcus, RobinsoniellaandClostridiumIV are associated with the ability to self-administer cocaine.

Associations between the gut microbiome and IVSA acquisition are sex-specific. Decreased relative abundances ofLactobacillus and Blautiaare associated with IVSA in male and female mice, respectively.

The relative abundances ofRobinsoniellaandClostridiumIV were correlated with the number of infusions of self-administered cocaine.

Functional potential analysis of the gut microbiome supports a role for microbiomes encoding glutamate metabolism in the ability to self-administer cocaine.
An impedance-based chemiresistor for the real-time detection of gut microbiota-generated short-chain fatty acids
Authors: Yavarinasab Adel , Flibotte Stephane , Liu Sijie , Tropini Carolina
Published: September 2022

Short-chain fatty acids (SCFAs) are key molecules produced by gut bacteria in the intestine, that are absorbed into the bloodstream and strongly influence human health. SCFA disruption and imbalances have been linked to many diseases; however, they are seldom used diagnostically as their detection requires extensive sample preparation and expensive equipment. In this work, an electrochemical sensor was developed to enable real-time, quantitative measurement of SCFAs from complex samples in liquid phase without the need for extraction, evaporation, or destruction. An impedance-based sensor for in vitro detection of acetic acid, propionic acid, and butyric acid (accounting for more than 95% of SCFAs in the intestine) was fabricated by the deposition of a ZnO and polyvinyl alcohol (PVA) on the surface of a microfabricated interdigitated gold electrode. The sensor was first exposed to a broad, physiologically relevant range of concentrations of SCFAs in isolation (0.5–20 mg/ml) and unlike previously published SCFA sensors that could detect only in gas form with the aid of evaporation, it was able to detect them directly in the liquid phase at room temperature. Electrochemical impedance spectroscopy analysis was then applied to the mixture of SCFAs prepared at different ratios and in complex media at concentrations ranging from 0.5 to 10 mg/ml, which showed the capability of the sensor to measure SCFAs in experimentally relevant mixture. The recorded faradaic responses were then used to train a fit-to-data model to utilize the sensor to screen human bacterial isolates and detect which species secrete SCFAs in vitro. This work will allow for the rapid and non-destructive determination of the levels of SCFAs in complex biological samples, providing a miniaturized, highly stable, and highly sensitive sensor for real-time monitoring applications.
Development of a High-Performance Open-Source 3D Bioprinter
Authors: Tashman Joshua W. , Shiwarski Daniel J. , Feinberg Adam W.
Published: September 2022

The application of 3D printing to biological research has provided the tissue engineering community with a method for organizing cells and biological materials into complex 3D structures. While many commercial bioprinting platforms exist, they are expensive, ranging from $5,000 to over $500,000. This high cost of entry prevents many labs from incorporating 3D bioprinting into their research. Due to the open-source nature of desktop plastic 3D printers, an alternative option has been to convert low-cost plastic printers into bioprinters. Several open-source modifications have been described, but there remains a need for a user-friendly, step-by-step guide for converting a thermoplastic printer into a bioprinter using components with validated performance. Here we convert a low-cost 3D printer, the FlashForge Finder, into a bioprinter using our Replistruder 4 syringe pump and the Duet3D Duet 2 WiFi for total cost of less than $900. We demonstrate that the accuracy of the bioprinter’s travel is better than 35 µm in all three axes, and quantify fidelity by printing square lattice collagen scaffolds with average errors less than 2%. We also show high fidelity reproduction of clinical-imaging data by printing a scaffold of a human ear using collagen bioink. Finally, to maximize accessibility and customizability, all components we have designed for the bioprinter conversion are provided as open-source 3D models, along with instructions for further modifying the bioprinter for additional use cases, resulting in a comprehensive guide for the bioprinting field.
Huntingtin Over-Expression Does Not Alter Overall Survival in Murine Cancer Models
Authors: Chan Laura , Hill Austin , Lu Ge , Van Raamsdonk Jeremy , Gascoyne Randy D. , Hayden Michael R. , Leavitt Blair R.
Published: September 2022

A reduced incidence of various forms of cancer has been reported in Huntington’s disease (HD) patients and may be due to pro-apoptotic effects of mutant huntingtin. We tested this hypothesis by assessing the effects of huntingtin protein over-expression on survival in two murine cancer models. We generated yeast artificial chromosome (YAC) HD mice containing human huntingtin transgenes with various CAG tract lengths (YAC18, YAC72, YAC128) on either an Msh2 or p53 null background, which have increased cancer incidence. In both mouse models of cancer, the over-expression of either mutant or wild-type huntingtin had no significant effect on overall survival. These results do not support the hypothesis that mutant huntingtin expression is protective against cancer.
Treatment with anti-HER2 chimeric antigen receptor tumor-infiltrating lymphocytes (CAR-TILs) is safe and associated with antitumor efficacy in mice and companion dogs
Authors: Forsberg Elin MV , Riise Rebecca , Saellström Sara , Karlsson Joakim , Alsén Samuel , Bucher Valentina , Hemminki Akseli , Olofsson Bagge Roger , Ny Lars , Nilsson Lisa M , Rönnberg Henrik , Nilsson Jonas A
Published: September 2022

Patients with metastatic melanoma have a historically poor prognosis, but recent advances in treatment options, including targeted therapy and immunotherapy, have drastically improved the outcomes for some of these patients. However, not all patients respond to available treatments, and around 50% of patients with metastatic cutaneous melanoma and almost all patients with metastases of uveal melanoma die of their disease. Thus, there is a need for novel treatment strategies for patients with melanoma that do not benefit from the available therapies. Chimeric antigen receptor-expressing T (CAR-T) cells are largely unexplored in melanoma. Traditionally, CAR-T cells have been produced by transducing blood-derived T cells with a virus expressing CAR. However, tumor-infiltrating lymphocytes (TILs) can also be engineered to express CAR, and such CAR-TILs could be dual-targeting. To this end, tumor samples and autologous TILs from metastasized human uveal and cutaneous melanoma were expanded in vitro and transduced with a lentiviral vector encoding an anti-HER2 CAR construct. When infused into patient-derived xenograft (PDX) mouse models carrying autologous tumors, CAR-TILs were able to eradicate melanoma, even in the absence of antigen presentation by HLA. To advance this concept to the clinic and assess its safety in an immune-competent and human-patient-like setting, we treated four companion dogs with autologous anti-HER2 CAR-TILs. We found that these cells were tolerable and showed signs of anti-tumor activity. Taken together, CAR-TIL therapy is a promising avenue for broadening the tumor-targeting capacity of TILs in patients with checkpoint immunotherapy-resistant melanoma.
Perturbation of Lipid Bilayers by Biomimetic Photoswitches Based on Cyclocurcumin
Authors: Delova Anastasiia , Losantos Raúl , Pecourneau Jérémy , Bernhard Yann , Mourer Maxime , Pasc Andreea , Monari Antonio
Published: September 2022

The use of photoswitches which may be activated by suitable electromagnetic radiation is an attractive alternative to conventional photodynamic therapy. Here we report all atom molecular dynamics simulation of a biomimetic photoswitch derived from cyclocurcumin and experiencingE/Zphotoisomerization. In particular, we show that the two isomers interact persistently with a lipid bilayer modeling a cellular membrane. Furthermore, the interaction with the membrane is strongly dependent on the concentration and a transition between ordered or disordered arrangements of the photoswitches is observed. We also confirm that the structural parameters of the bilayer are differently affected by the two isomers, and hence can be modulated through photoswitching, offering interesting perspectives for future applications.

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The Chalcidoidea bush of life – a massive radiation blurred by mutational saturation
Authors: Cruaud Astrid , Rasplus Jean-Yves , Zhang Junxia , Burks Roger , Delvare Gérard , Fusu Lucian , Gumovsky Alex , Huber John T. , Janšta Petr , Mitroiu Mircea-Dan , Noyes John S. , van Noort Simon , Baker Austin , Böhmová Julie , Baur Hannes , Blaimer Bonnie B. , Brady Seán G. , Bubeníková Kristýna , Chartois Marguerite , Copeland Robert S. , Papilloud Natalie Dale-Skey , Dal Molin Ana , Dominguez Chrysalyn , Gebiola Marco , Guerrieri Emilio , Kresslein Robert L. , Krogmann Lars , Lemmon Emily Moriarty , Murray Elizabeth A. , Nidelet Sabine , Nieves-Aldrey José Luis , Perry Ryan K. , Peters Ralph S. , Polaszek Andrew , Sauné Laure , Torréns Javier , Triapitsyn Serguei , Tselikh Ekaterina V. , Yoder Matthew , Lemmon Alan R. , Woolley James B. , Heraty John M.
Published: September 2022

Capturing phylogenetic signal from a massive radiation can be daunting. The superfamily Chalcidoidea is an excellent example of a hyperdiverse group that has remained recalcitrant to phylogenetic resolution. Chalcidoidea are mostly parasitoid wasps that until now included 27 families, 87 subfamilies and as many as 500,000 estimated species. We combined 1007 exons obtained with Anchored Hybrid Enrichment with 1048 Ultra-Conserved Elements (UCEs) for 433 taxa including all extant families, over 95% of all subfamilies and 356 genera chosen to represent the vast diversity of the superfamily. Going back and forth between molecular results and our collective morphological and biological knowledge, we detected insidious bias driven by the saturation of nucleotide data and highlighted morphological convergences. Our final results are based on a concatenated analysis of the least saturated exons and UCE data sets (2054 loci, 284,106 sites). Our analyses support a sister relationship with Mymarommatoidea. Seven of the previously recognized families were not monophyletic, so foundations for a new classification are discussed. Biology appears potentially more informative than morphology, as illustrated by the elucidation of a clade of plant gall associates and a clade of taxa with planidial first-instar larvae. The phylogeny suggests a shift from smaller soft-bodied wasps to larger and more heavily sclerotized wasps. Deep divergences in Chalcidoidea coincide with an increase in insect families in the fossil record, and an early shift to phytophagy corresponds with the beginning of the “Angiosperm Terrestrial Revolution”. Our dating analyses suggest a Middle Jurassic origin of 174 Ma (167.3-180.5 Ma) and a crown age of 162.2 Ma (153.9–169.8 Ma) for Chalcidoidea. During the Cretaceous, Chalcidoidea underwent a rapid radiation in southern Gondwana with subsequent dispersals to the Northern Hemisphere. This scenario is discussed with regard to knowledge about host taxa of chalcid wasps, their fossil record, and Earth’s paleogeographic history.
Leadership in PhD (LeaP): a longitudinal leadership skill building program for underrepresented biomedical research trainees
Authors: Doles Mali D , Kang Ji Yun , Scholl Linda M , Doles Jason D
Published: September 2022

Abstract

Increasing diversity in the biomedical research workforce is a critical national issue. Particularly concerning is the lack of representation at more advanced career stages/in leadership positions. While there are numerous institutional initiatives promoting professional research skills (i.e. grant writing, presenting, networking) for underrepresented (UR) PhD trainees, there are comparatively fewer opportunities for leadership development. We present a blueprint for Leadership in PhD (LeaP), a cohort-based program aiming to equip UR biomedical research trainees with skills to succeed as academic, industry, and community leaders. In contrast to intensive short-term programs or workshops, LeaP is a longitudinal 4-year experience with an emphasis on self-directed and experiential learning. First year trainees receive foundational didactic instruction on core leadership concepts coupled with facilitated peer discussions and one-on-one coaching support. We outline a program evaluation framework that assesses student learning, satisfaction, and program efficacy. Evaluation data from the inaugural year is presented and discussed.
Defining Cardiac Recovery at Single Cell Resolution
Authors: Amrute Junedh M. , Lai Lulu , Ma Pan , Koenig Andrew L. , Kamimoto Kenji , Bredemeyer Andrea , Shankar Thirupura S. , Kuppe Christoph , Kadyrov Farid F. , Schulte Linda J. , Stoutenburg Dylan , Kopecky Benjamin J. , Navankasattusas Sutip , Visker Joseph , Morris Samantha A. , Kramann Rafael , Leuschner Florian , Mann Douglas L. , Drakos Stavros G. , Lavine Kory J.
Published: September 2022

Recovery of cardiac function is the ultimate goal of heart failure therapy. Unfortunately, cardiac recovery remains a rare and poorly understood phemomenon. Herein, we performed single nucleus RNA-sequencing (snRNA-seq) from non-diseased donors and heart failure patients. By comparing patients who recovered LV systolic function following LV assist device implantation to those who did not recover and donors, we defined the cellular and transcriptional landscape and predictors of cardiac recovery. We sequenced 40 hearts and recovered 185,881 nuclei with 13 distinct cell types. Using pseudobulk differential expression analysis to explicate cell specific signatures of cardiac recovery, we observed that recovered cardiomyocytes do not revert to a normal state, and instead, retain transcriptional signatures observed in heart failure. Macrophages and fibroblasts displayed the strongest signatures of recovery. While some evidence of reversion to a normal state was observed, many heart failure associated genes remained elevated and recovery signatures were predominately indicative of a biological state that was unique from donor and heart failure conditions. Acquisition of recovery states was associated with improved LV systolic function. Pro-inflammatory macrophages and inflammatory signaling in fibroblasts were identified as negative predictors of recovery. We identified downregulation of RUNX1 transcriptional activity in macrophages and fibroblasts as a central event associated with and predictive of cardiac recovery. In silico perturbation of RUNX1 in macrophages and fibroblasts recapitulated the transcriptional state of cardiac recovery. This prediction was corroborated in a mouse model of cardiac recovery mediated by BRD4 inhibition where we observed a decrease in macrophage and fibroblast Runx1 expression, diminished chromatin accessibility within peaks linked to the Runx1 locus, and acquisition of recovery signatures. These findings suggest that cardiac recovery is a unique biological state and identify RUNX1 as a possible therapeutic target to facilitate cardiac recovery.
Detecting stabilizing, directional, and disruptive patterns of anthropogenic species loss with general models of nonrandom extinction
Authors: Huron Nicholas A. , Hedges S. Blair , Helmus Matthew R.
Published: September 2022

The selective landscape that gave rise to Earth’s species has shifted in the Anthropocene. Humans have accelerated extinction pressures, making efforts to detect general non-random patterns of extinction increasingly important. Much research has focused on detecting which traits make some species more likely to go extinct, such as large body size and slow reproductive rate in animals, limited dispersal in vascular plants, and narrow habitat requirements in cacti. However, general models for such non-random extinction are lacking. Here, we adapt the three general models of natural selection to classify non-random extinction as directional, disruptive, or stabilizing extinction. We develop a quantitative method for testing which general extinction model best describes observed data and apply it to the Caribbean lizard genusLeiocephalusas a case study. We surveyed the literature for recorded last occurrence for extinct and threat status for extant species. Eight species have gone extinct and ten are predicted to go extinct soon. Past extinctions inLeiocephalusshowed directional extinction of large bodied species, while future-predicted extinctions exhibited a more complex extinction model similar to both random and stabilizing extinction with respect to body size. Similarly, future-predicted extinctions exhibited stabilizing extinction with respect to limb and tail lengths. Lizards with either very long or very short appendages are most likely to go extinct in the future. This shift from directional to stabilizing extinction forLeiocephalusis consistent with hunting, introduced predators, and habitat loss that first increased extinction pressure on the largest species and then extinction pressure on species that deviate from an adaptive peak centered on a generalist ground-lizard body plan. As adaptive optima shift in the Anthropocene, general models of non-random extinction are essential to developing a mature strategy for future successful conservation efforts.
High Resolution Imaging of the Osteogenic and Angiogenic Interface at the Site of Cranial Bone Defect Repair via Multiphoton Microscopy
Authors: Schilling Kevin , Zhai Yuankun , Zhou Zhuang , Zhou Bin , Brown Edward , Zhang Xinping
Published: September 2022

The spatiotemporal blood vessel formation and specification at the osteogenic and angiogenic interface of cranial bone defect repair were examined utilizing a high-resolution multiphoton-based imaging platform in conjunction with advanced optical techniques that allow interrogation of the oxygen microenvironment and cellular energy metabolism in living animals. Our study demonstrates the dynamic changes of vessel types, i.e. arterial, venous and capillary vessel networks at the superior and dura periosteum of cranial bone defect, suggesting a differential coupling of the vessel type with osteoblast expansion and bone tissue deposition/remodeling during repair. Employing transgenic reporter mouse models that label distinct types of vessels at the site of repair, we further show that oxygen distributions in capillary vessels at the healing site are heterogeneous as well as time and location-dependent. The endothelial cells coupling to osteoblasts prefer glycolysis and are less sensitive to microenvironmental oxygen changes than osteoblasts. In comparison, osteoblasts utilize relatively more OxPhos and potentially consume more oxygen at the site of repair. Taken together, our study highlights the dynamics and functional significance of blood vessel types at the site of defect repair, opening up opportunities for further delineating the oxygen and metabolic microenvironment at the interface of bone tissue regeneration.
Ensemble Machine Learning to “Boost” Ubiquitination-sites Prediction
Authors: Mo Xiaoye , Jiang Xia
Published: September 2022

Ubiquitination-site prediction is an important task because ubiquitination is a critical regulatory function for many biological processes such as proteasome degradation, DNA repair and transcription, signal transduction, endocytoses, and sorting. However, the highly dynamic and reversible nature of ubiquitination makes it difficult to experimentally identify specific ubiquitination sites. In this paper, we explore the possibility of improving the prediction of ubiquitination sites using ensemble machine learning methods including Random Forrest (RF), Adaptive Boosting (ADB), Gradient Boosting (GB), and eXtreme Gradient Boosting (XGB). By doing grid search with the four ensemble methods and six comparison non-ensemble learning methods including Naïve Base (NB), Logistic Regression (LR), Decision Trees (DT), Support Vector Machine (SVM), LASSO, and K-Nearest Neighbor (KNN), we find that all the four ensemble methods significantly outperform one or more non-ensemble methods included in this study. XGB outperforms three out of the six non-ensemble methods that we included; ADB and RF both outperform two of the six non-ensemble methods; GB outperforms one non-ensemble method. Comparing the four ensemble methods among themselves. GB performs the worst; XGB and ADB are very comparable in terms of prediction, but ADB beats XGB by far in terms of both the unit model training time and total running time. Both XGB and ADB tend to do better than RF in terms of prediction, but RF has the shortest unit model training time out of the three. In addition, we notice that ADB tends to outperform XGB when dealing with small-scale datasets, and RF can outperform either ADB or XGB when data are less balanced. Interestingly, we find that SVM, LR, and LASSO, three of the six non-ensemble methods included, perform comparably with all the ensemble methods. Based on this study, ensemble learning is a promising approach to ignificantly improving ubiquitination-site prediction using protein segment data.