bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractIn 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

AbstractThe 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

AbstractThe 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

AbstractThe 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

AbstractClam 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

AbstractRhythmic 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

AbstractCurrent 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

AbstractAlterations 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

AbstractAdoptive 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

AbstractThe 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

AbstractThe 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.HIGHLIGHTSCorrelational 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

AbstractShort-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.