bluuebunny/crossref_metadata_2025_split huggingface dataset:
Species interactions and diversity: a unified framework using Hill numbers
Authors: Godsoe William , Murray Rua , Iritani Ryosuke 
Published: October 2022

AbstractBiodiversity describes the variety of organisms on planet earth. Ecologists have long hoped for a synthesis between analyses of biodiversity and analyses of biotic interactions among species, such as predation, competition, and mutualism. However, it is often unclear how to connect details of these interactions with complex modern analyses of biodiversity. To resolve this gap, we propose a unification of models of biotic interactions and measurements of diversity. We show that analyses of biodiversity obscure details about biotic interactions. For example, identical changes in biodiversity can arise from predation, competition or mutualism. Our approach indicates that traditional models of community assembly miss key facets of diversity change. Instead, we suggest that analyses of diversity change should focus on partitions, which measure mechanisms that directly shape changes in diversity, notably species level selection and immigration, rather than traditional analyses of biotic interactions.SpeculationsOur paper proposes that observations of biodiversity cannot be used to distinguish different types of biotic interactions. For generations ecologists have been fascinated with the links between biodiversity and biotic interactions (i.e. competition, mutualism and predation). Many of us expect that observations of biodiversity provide vital clues about how biotic interactions operate in nature, but it is hard to tell when these clues are reliable.Our work integrates models of biotic interactions and measurements of biodiversity diversity change. This highlights how an observed change in diversity can be compatible with any type of biotic interaction (i.e. competition, mutualism, predation etc.). So for example, the same increase in Shannon diversity could indicate the superior ability of a competitor the success of mutualists or a predator’s tendency to harvest dominant prey species. This is so because diversity measures are designed to be concerned with changes in relative abundances but not account for absolute abundance changes.Observations of biodiversity change are unlikely to yield insights about biotic interactions per se because biodiversity itself obscures species’ absolute abundances. Therefore, models of diversity change should focus on mechanisms that are less influenced by changes in absolute abundances such as species-level selection.
Throat colour polymorphism in relation to sex and body size of the Litter skink,Lankascincus fallax
Authors: Jayamanna J.M.A. Ishara K. , de Silva Anslem , Ukuwela Kanishka D.B. 
Published: October 2022

ABSTRACTColour polymorphism is a pervasive phenomenon in both animal and plant kingdoms and understanding its evolution and maintenance is of great interest. Among the lizards of Sri Lanka, the endemic skinkLankascincus fallaxshows throat colour polymorphism in which, the underlying basis is not clearly known. In this study, we examined the relationship of the three different throat colour morphs observed in this species with the sex, body size and the geographic location ofL. fallax. Live skinks were sampled from two locations in Sri Lanka and sex and the throat colour was categorized visually and the snout to vent length (SVL) was measured. Tail tips of some selected individuals from the two locations were taken and a fragment of the 12S rRNA gene was sequenced in representative individuals having the different throat colour morphs. Pairwise genetic distance of the three colour morphs ranged between 0.4–0.5% confirming that the three colour morphs were the same species. Three colour morphs (red, black and white) were observed in males in both locations, while only the white morph was observed in females, suggesting that the throat color polymorphism was confined to males. There was a significant difference between the mean SVL of males with red and black throat colours (39.35 mm) and males with white throat colours (30.31 mm). Thus, the study suggests that the throat colour in these skinks is highly associated with sex and the body size in males. The study further suggests thatL. fallaxis sexually dichromatic and that the males show throat colour polymorphism. However, future studies are necessary to understand the underlying drivers for the presence and maintenance of sexual dichromatism and throat colour polymorphism inL. fallax.
Temporal Application of Lysyl Oxidase during Hierarchical Collagen Fiber Formation Differentially Effects Mechanics in Engineered Tissues
Authors: Bates Madison , Troop Leia , Brown M. Ethan , Puetzer Jennifer L. 
Published: October 2022

AbstractThe primary source of strength in musculoskeletal menisci, tendons, and ligaments are hierarchical collagen fibers; however, these fibers are not regenerated after injury nor in engineered replacements, resulting in limited repair options. Collagen strength is reliant on fiber alignment, density, diameter, and crosslinking. Recently, we developed a culture system which guides cells in high-density collagen gels to develop native-like hierarchically organized collagen fibers, which match native alignment and fiber diameters by 6 weeks. However, tissue mechanics plateau at 1 MPa, suggesting crosslinking is lacking. Collagen crosslinking is regulated by lysyl oxidase (LOX) which forms immature crosslinks that condense into mature trivalent crosslinks. Trivalent crosslinks are thought to be the primarily source of strength in fibers, but its not well understood how they form. The objective of this study was to evaluate the effect of exogenous LOX treatment at different stages of hierarchical fiber formation in our culture system to produce functional engineered replacements and to better understand factors effecting collagen crosslink maturation. We found LOXL2 treatment did not restrict hierarchical fiber formation, with constructs still forming aligned collagen fibrils by 2 weeks, larger fibers by 4 weeks, and early fascicles by 6 weeks. However, LOXL2 treatment did significantly increase mature pyridinium crosslink accumulation and tissue mechanics, with timing of LOXL2 supplementation during fiber formation having a significant effect. Overall, we found one week of LOXL2 supplementation at 4 weeks produced constructs with native fiber organization, increased PYD accumulation, and increased mechanics, ultimately matching the tensile modulus of immature bovine menisci.Statement of SignificanceCollagen fibers are the primarily source of strength and function in connective tissues throughout the body, however it remains a challenge to develop these fibers in engineered replacements, greatly reducing treatment options. Here we demonstrate lysyl oxidase like 2 (LOXL2) can be used to significantly improve the mechanics of tissue engineered constructs, but timing of application is important and will most likely depend on degree of collagen organization or maturation. Currently there is limited understanding of how collagen crosslinking is regulated, and this system is a promising platform to further investigate cellular regulation of LOX crosslinking. Understanding the mechanism that regulates LOX production and activity is needed to ultimately regenerate functional repair or replacements for connective tissues throughout the body.
A germline-targeting chimpanzee SIV envelope glycoprotein elicits a new class of V2-apex directed cross-neutralizing antibodies
Authors: Bibollet-Ruche Frederic , Russell Ronnie M. , Ding Wenge , Liu Weimin , Li Yingying , Wagh Kshitij , Wrapp Daniel , Habib Rumi , Skelly Ashwin N. , Roark Ryan S. , Sherrill-Mix Scott , Wang Shuyi , Rando Juliette , Lindemuth Emily , Cruickshank Kendra , Park Younghoon , Baum Rachel , Connell Andrew Jesse , Li Hui , Giorgi Elena E. , Song Ge S. , Ding Shilei , Finzi Andrés , Newman Amanda , Hernandez Giovanna E. , Machiele Emily , Cain Derek W. , Mansouri Katayoun , Lewis Mark G. , Montefiori David C. , Wiehe Kevin J. , Alam S. Munir , Teng I-Ting , Kwong Peter D. , Andrabi Raiees , Verkoczy Laurent , Burton Dennis R. , Korber Bette T. , Saunders Kevin O. , Haynes Barton F. , Edwards Robert J. , Shaw George M. , Hahn Beatrice H. 
Published: October 2022

AbstractHIV-1 and its SIV precursors share a broadly neutralizing antibody (bNAb) epitope in variable loop 2 (V2) at the envelope glycoprotein (Env) trimer apex. Here, we tested the immunogenicity of germline-targeting versions of a chimpanzee SIV (SIVcpz) Env in human V2-apex bNAb heavy-chain precursor-expressing knock-in mice and as chimeric simian-chimpanzee immunodeficiency viruses (SCIVs) in rhesus macaques (RMs). Trimer immunization of knock-in mice induced V2-directed NAbs, indicating activation of V2-apex bNAb precursor-expressing mouse B cells. SCIV infection of RMs elicited high-titer viremia, potent autologous tier 2 neutralizing antibodies, and rapid sequence escape in the canonical V2-apex epitope. Six of seven animals also developed low-titer heterologous plasma breadth that mapped to the V2-apex. Antibody cloning from two of these identified multiple expanded lineages with long heavy chain third complementarity determining regions that cross-neutralized as many as 7 of 19 primary HIV-1 strains, but with low potency. Negative stain electron microscopy (NSEM) of members of the two most cross-reactive lineages confirmed V2 targeting but identified an angle of approach distinct from prototypical V2-apex bNAbs, with antibody binding either requiring or inducing an occluded-open trimer. Probing with conformation-sensitive, non-neutralizing antibodies revealed that SCIV-expressed Envs as well as some primary HIV-1 Envs adopted a more open conformation, thereby exposing a conserved V2 epitope that is occluded in closed SIVcpz and HIV-1 Env trimers. These results expand the spectrum of V2-apex targeted antibodies that can contribute to neutralization breadth and identify novel SIV Env platforms for further development as germline-targeting and immunofocusing immunogens.One sentence summaryA cryptic V2 epitope in occluded-open HIV and SIV Env trimers is the target of a new class of V2-directed cross-neutralizing antibodies.
Automating microbial taxonomy workflows with PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes
Authors: Wirth Joseph S. , Bush Eliot C. 
Published: October 2022

AbstractThe nucleotide sequences of 16S ribosomal RNA (rRNA) genes have been used to inform the taxonomic placement of prokaryotes for several decades. Whole-genome approaches can better resolve evolutionary relationships of organisms, but these analyses often require computational proficiencies that are uncommon among microbiologists. PHANTASM is a new tool capable of automating these workflows. This tool was designed to work for a wide range of prokaryotes and is the first example of an automated reconciliation of NCBI’s Taxonomy database with that of the List of Prokaryotic names with Standing in Nomenclature (LPSN). In this study, we describe the workflow of PHANTASM and provide several examples of results generated by it. The source code is freely-available on GitHub. In order to facilitate the ease-of-access for researchers, PHANTASM is also available as a Docker image. While other tools exist to facilitate starting points for these analyses, PHANTASM provides users with a greater degree of control and produces outputs that can be used to make publication-quality figures.
A Chromosome-length Assembly of the Black Petaltail (Tanypteryx hageni) Dragonfly
Authors: Tolman Ethan R. , Beatty Christopher D. , Bush Jonas , Kohli Manpreet , Moreno Carlos M. , Ware Jessica L. , Weber K. Scott , Khan Ruqayya , Maheshwari Chirag , Weisz David , Dudchenko Olga , Aiden Erez Lieberman , Frandsen Paul B. 
Published: October 2022

AbstractWe present a chromosome-length genome assembly and annotation of the Black Petaltail dragonfly (Tanypteryx hageni). This habitat specialist diverged from its sister species over 70 million years ago, and separated from the most closely related Odonata with a reference genome 150 million years ago. Using PacBio HiFi reads and Hi-C data for scaffolding we produce one of the most high quality Odonata genomes to date. A scaffold N50 of 206.6 Mb and a BUSCO score of 96.8% indicate high contiguity and completeness.SignificanceWe provide a chromosome-length assembly of the Black Petaltail dragonfly (Tanypteryx hageni), the first genome assembly for any non-libelluloid dragonfly. The Black Petaltail diverged from its sister species over 70 million years ago.T. hageni, like its confamilials, occupies fen habitats in its nymphal stage, a life history uncommon in the vast majority of dragonflies. We hope that the availability of this assembly will facilitate research onT. hageniand other petaltail species, to better understand their ecology and support conservation efforts.
Early life sleep disruption has long lasting, sex specific effects on later development of sleep in prairie voles
Authors: Jones-Tinsley Carolyn E. , Olson Randall J. , Mader Miranda , Wickham Peyton T. , Gutowsky Katelyn , Wong Claire , Chu Sung Sik , Milman Noah E. , Cao Hung , Lim Miranda M. 
Published: October 2022

ABSTRACTIn mammals, sleep duration is highest in the early postnatal period of life and is critical for shaping neural circuits that control the development of complex behaviors. The prairie vole is a wild, highly social rodent that serves as a unique model for the study of complex, species-typical social behaviors. Previous work in our laboratory has found that early life sleep disruption (ELSD) in prairie voles during a sensitive window of postnatal development leads to long lasting changes in social and cognitive behaviors as well as structural changes in excitatory and inhibitory neural circuits in the brain. However, it is currently unknown how later sleep is impacted by ELSD, both shortly after ELSD and over the long term. Therefore, the aim of this study was to describe the effects of ELSD on later life sleep, compared to sleep in normally developing prairie voles. First, we conducted tethered electroencephalogram/electromyogram (EEG/EMG) recordings in juvenile prairie voles undergoing ELSD, compared to Control conditions. Second, we conducted 24 hours of home cage tethered EEG/EMG recordings in either adolescent or adult male and female prairie voles that had previously undergone ELSD or Control conditions as juveniles. We found that, as adults, male ELSD prairie voles showed persistently lower REM sleep duration and female ELSD prairie voles showed persistently higher NREM sleep duration compared to Controls, but no other sleep parameters differed. We concluded that 1) persistent effects of ELSD on sleep into adulthood may contribute to the social and cognitive deficits observed in adult voles, and 2) sleep disruption early in life can influence later sleep patterns in adulthood.
Indications of an Achaea sp. caterpillar outbreak disrupting fruiting of an ectomycorrhizal tropical tree in Central African rainforest
Authors: Norghauer Julian M. , Newbery David M. , Neba Godlove A. 
Published: October 2022

ABSTRACTBackground and aimsWhere one or several tree species come to dominate patches of tropical forest, as many masting ectomycorrhizal legumes do in central Africa, ecological theory predicts they may be prone to herbivory which might alter their reproductive output. This was indirectly investigated in lowland rainforest in Cameroon forTetraberlinia korupensis, whose crowns were attacked in 2008 by an outbreaking black caterpillar—identified as anAchaeasp., probablyA. catocaloides—in Korup National Park.Material and methodsField-collected data on tree-level seed and fruit (pod) production ofT. korupensisin its 2008 masting event were compared with that of its two co-dominant neighbours (T. bifoliolata, Microberlinia bisulcata) whose populations masted in 2007 (and 2010). To do this, bivariate regression models (linear, polynomial, ZiG [zero-inflated gamma model]), contingency table analysis, and non-parametric measures of dispersion were used.Key resultsAssumingT. korupensisis prone toAchaeacaterpillar attacks, empirical data support the hypothesized lower proportion of adults participating in its masting (54% in 2008) than for either masting population ofM. bisulcata(98% in 2007, 89% in 2010) orT. bifoliolata(96% in 2007, 78% in 2010). These fruitingT. korupensistrees were about one-third larger in stem diameter than conspecific non-fruiters and produced as many pods and seeds per capita asT. bifoliolata. But regressions only modestly support the hypothesis that the positive tree size–fecundity relationship forT. korupensiswas weaker (i.e., lower adj.R2) than forM. bisulcata(whose leaves are morphologically similar) orT. bifoliolata, with mostly similar dispersion about the median among these species.ConclusionAltogether, the findings suggest a role for tolerance in nutrient-poor forests. It is postulated that instead of conferring resistance to herbivores, the ectomycorrhizas associated with these trees may enable them to more quickly recover from potential yet unpredictable insect outbreaks.
Enhancing functionalized liposome avidity to cells via lipid phase separation
Authors: Vu Timothy Q. , Sant’Anna Lucas E. , Kamat Neha P. 
Published: October 2022

ABSTRACTThe addition of both cell-targeting moieties and polyethylene glycol (PEG) to nanoparticle (NP) drug delivery systems is a standard approach to improve the biodistribution, specificity, and uptake of therapeutic cargo. The spatial presentation of these molecules affects avidity of the NP to target cells in part through an interplay between the local ligand concentration and the steric hindrance imposed by PEG molecules. Here, we show that lipid phase separation in nanoparticles can modulate liposome avidity by changing the proximity of PEG and targeting protein molecules on a nanoparticle surface. Using lipid-anchored nickelnitrilotriacetic acid (Ni-NTA) as a model ligand, we demonstrate that the attachment of lipid anchored Ni-NTA and PEG molecules to distinct lipid domains in nanoparticles can enhance liposome binding to cancer cells by increasing ligand clustering and reducing steric hindrance. We then use this technique to enhance the binding of RGD-modified liposomes, which can bind to integrins overexpressed on many cancer cells. These results demonstrate the potential of lipid phase separation to modulate the spatial presentation of targeting and shielding molecules on nanocarriers, offering a powerful tool to enhance the efficacy of NP drug delivery systems.
IL-6/STAT3 signaling drives early-stage pancreatic cancer cachexia via suppressed ketogenesis
Authors: Arneson-Wissink Paige C. , Mendez Heike , Pelz Katherine , Dickie Jessica , Bartlett Alexandra Q. , Worley Beth L. , Krasnow Stephanie M. , Eil Robert , Grossberg Aaron J. 
Published: October 2022

SUMMARYCancer cachexia is highly prevalent in patients with pancreatic ductal adenocarcinoma (PDAC). Although advanced cachexia is associated with inflammatory signaling, the early events driving wasting are poorly defined. Using an orthotopic mouse model of PDAC, we find that early cachexia is defined by a pronounced vulnerability to undernutrition, characterized by increased skeletal muscle wasting. PDAC suppresses lipid beta oxidation and impairs ketogenesis in the liver, which coordinates the adaptive response to nutritional scarcity. When PDAC mice are fed ketogenic diet, this effect is reversed, and muscle mass is preserved. Furthermore, physiologic levels of ketones are sufficient to protect myotubes against PDAC-associated wasting. Interleukin-6 (IL-6) drives liver metabolic reprogramming, and hepatocyte-specific loss of Signal Transducer and Activator of Transcription 3 (STAT3) is sufficient to prevent PDAC-associated muscle loss. Together, these studies define a key role for the liver in cachexia development and directly link skeletal muscle homeostasis to hepatic lipid oxidation.
Thousandfold Cell-Specific Pharmacology of Neurotransmission
Authors: Shields Brenda C. , Yan Haidun , Lim Shaun S.X. , Burwell Sasha C. , Fleming Elizabeth A. , Cammarata Celine M. , Kahuno Elizabeth W. , Vagadia Purav P. , Loughran Marie H. , Zhiquan Lei , McDonnell Mark E. , Scalabrino Miranda L. , Thapa Mishek , Hawley Tammy M. , Reitz Allen B. , Schiltz Gary E. , Hull Court , Field Greg D. , Glickfeld Lindsey L. , Tadross Michael R. 
Published: October 2022

SUMMARYCell-specific pharmaceutical technologies promise mechanistic insight into clinical drugs―those that treat, and often define, human disease. In particular,DART(drug acutely restricted by tethering) achieves genetically programmable control of drug concentration over cellular dimensions. The method is compatible with clinical pharmaceuticals and amenable to studies in behaving animals. Here, we describeDART.2, comprising three advances. First, we improve the efficiency of chemical capture, enabling cell-specific accumulation of drug to ∼3,000-times the ambient concentration in 15 min. Second, we develop tracer reagents, providing a behavior-independent measure of cellular target engagement in each animal. Third, we extend the method to positive allosteric modulators and outline design principles for this clinically significant class. We showcase the platform with four pharmaceuticals―two that weaken excitatory (AMPAR) or inhibitory (GABAAR) chemical neurotransmission, and two that strengthen these forms of synaptic communication. Across four labs, we tested reagents in the mouse cerebellum, basal ganglia, visual cortex, and retina. Collectively, we demonstrate robust, bidirectional editing of chemical neurotransmission. We provide for distribution of validated reagents, community design principles, and synthetic building blocks for application to diverse pharmaceuticals.
Huntingtin expression influences spontaneous seizure disorder susceptibility in FVN/B mice
Authors: Van Raamsdonk Jeremy M. , Al-Shekeli Hilal , Wagner Laura , Bredy Tim W , Chan Laura , Pearson Jacqueline , Schwab Claudia , Murphy Zoe , Devon Rebecca S. , Lu Ge , Kobor Michael S. , Hayden Michael R. , Leavitt Blair R. 
Published: October 2022

ABSTRACTHuntington disease (HD) is an adult-onset neurodegenerative disorder that is caused by a trinucleotide CAG repeat expansion in the HTT gene that codes for the protein huntingtin (HTT or Htt in mice). HTT is a multi-functional, ubiquitously expressed protein that is essential for embryonic survival, normal neurodevelopment, and adult brain function. The ability of wild-type HTT to protect neurons against various forms of death raises the possibility that loss of normal HTT function may worsen disease progression in HD. Huntingtin-lowering therapeutics are being evaluated in clinical trials for HD, but concerns have been raised that decreasing wild-type HTT levels may have adverse effects. Here we show that Htt levels modulate the occurrence of an idiopathic seizure disorder that spontaneously occurs in FVB/N mice. These abnormal FVB/N mice demonstrate various cardinal features of mouse models of epilepsy including spontaneous seizures, astrocytosis, neuronal hypertrophy, upregulation of brain-derived neurotrophic factor (BDNF), and sudden seizure-related death. Interestingly, decreasing wild-type Htt levels increased the frequency of this disorder, while over-expression of HTT completely prevented it. Examination of the mechanism underlying huntingtin’s ability to modulate the frequency of this seizure disorder indicated that over-expression of full length HTT can promote neuronal survival following seizures. Overall, our results demonstrate a protective role for huntingtin in this form of epilepsy and provide a plausible explanation for the observation of seizures in the juvenile form of HD, Lopes-Maciel-Rodan syndrome, and Wolf-Hirschhorn syndrome. Adverse effects caused by altering huntingtin levels has ramifications related to Huntingtin-lowering therapies in development to treat HD.