bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complex vaccination strategies prevent the emergence of vaccine resistance
Authors: Rella Simon A , Kulikova Yuliya A , Minnegalieva Aygul R , Kondrashov Fyodor A 
Published: July 2024

Abstract
Vaccination is the most effective tool to control infectious diseases. However, the evolution of vaccine resistance, exemplified by vaccine resistance in SARS-CoV-2, remains a concern. Here, we model complex vaccination strategies against a pathogen with multiple epitopes—molecules targeted by the vaccine. We found that a vaccine targeting one epitope was ineffective in preventing vaccine escape. Vaccine resistance in highly infectious pathogens was prevented by the full-epitope vaccine, that is, one targeting all available epitopes, but only when the rate of pathogen evolution was low. Strikingly, a bet-hedging strategy of random administration of vaccines targeting different epitopes was the most effective in preventing vaccine resistance in pathogens with the low rate of infection and high rate of evolution. Thus, complex vaccination strategies, when biologically feasible, may be preferable to the currently used single-vaccine approaches for long-term control of disease outbreaks, especially when applied to livestock with near 100% vaccination rates.
Economic evaluation of reopening a dormant tree improvement programme: a case study with Scots pine in Scotland
Authors: Saraev Vadim , Ahtikoski Anssi , Whittet Richard , Ray Duncan 
Published: July 2024

Abstract
The deployment of improved forest reproductive material (FRM) selected to yield greater timber volume and quality than unimproved material could help to maintain productive, sustainable, and resilient forests and increase resistance to abiotic and biotic threats under extreme climate change events. In Scotland, Scots pine (Pinus sylvestris L.) is a productive species that aligns with these objectives. However, confidence in Scots pine has been low in recent years due to damage caused by the needle blight Dothistroma septosporum. Recent provenance/progeny trials using native Scots pine material from the Caledonian pine woods indicate a favourable genetic correlation between growth and resistance to D. septosporum, suggesting that simultaneous improvements are possible. The Scots pine breeding programme in Scotland was closed in 2002. Here, we present an economic case for reopening the breeding programme to further improve Scots pine FRM. Specifically, we evaluate the costs and potential benefits of supporting a new programme. We conduct an analysis using three improvement scenarios using a Faustmann formula (amended with thinnings) to maximize the land expectation value. Our results indicate that further improvement of Scots pine FRM would be cost-effective, outperforming the current Scots pine timber production and financial outcomes. The analysis shows that the Central scenario’s land expectation value rises by £883 ha−1 compared to the baseline of £79 ha−1, assuming a 3.5% interest rate. We employed both annuity calculations and a break-even analysis to show improved FRM could maintain a breeding programme investment of £3.5 million per year over a 30-year period with a break-even cost threshold increase of ~52% for purchasing improved planting materials from £0.33 to £0.50 per seedling. In conclusion, the study provides economic evidence of the commercial benefits for reopening the Scots pine breeding programme to increase timber production and financial returns.
Male-biased recombination at chromosome ends in a songbird revealed by precisely mapping crossover positions
Authors: Zhang Hongkai , Lundberg Max , Ponnikas Suvi , Hasselquist Dennis , Hansson Bengt 
Published: July 2024

Abstract
Recombination plays a crucial role in evolution by generating novel haplotypes and disrupting linkage between genes, thereby enhancing the efficiency of selection. Here, we analyze the genomes of 12 great reed warblers (Acrocephalus arundinaceus) in a 3-generation pedigree to identify precise crossover positions along the chromosomes. We located more than 200 crossovers and found that these were highly concentrated toward the telomeric ends of the chromosomes. Apart from this major pattern in the recombination landscape, we found significantly higher frequencies of crossovers in genic compared with intergenic regions, and in exons compared with introns. Moreover, while the number of recombination events was similar between the sexes, the crossovers were located significantly closer to the ends of paternal compared with maternal chromosomes. In conclusion, our study of the great reed warbler revealed substantial variation in crossover frequencies within chromosomes, with a distinct bias toward the sub-telomeric regions, particularly on the paternal side. These findings emphasize the importance of thoroughly screening the entire length of chromosomes to characterize the recombination landscape and uncover potential sex-biases in recombination.
Dynamic Expansions and Retinal Expression of Spectrally Distinct Short-Wavelength Opsin Genes in Sea Snakes
Authors: Rossetto Isaac H , Ludington Alastair J , Simões Bruno F , Van Cao Nguyen , Sanders Kate L 
Published: July 2024

Abstract
The photopigment-encoding visual opsin genes that mediate color perception show great variation in copy number and adaptive function across vertebrates. An open question is how this variation has been shaped by the interaction of lineage-specific structural genomic architecture and ecological selection pressures. We contribute to this issue by investigating the expansion dynamics and expression of the duplicated Short-Wavelength-Sensitive-1 opsin (SWS1) in sea snakes (Elapidae). We generated one new genome, 45 resequencing datasets, 10 retinal transcriptomes, and 81 SWS1 exon sequences for sea snakes, and analyzed these alongside 16 existing genomes for sea snakes and their terrestrial relatives. Our analyses revealed multiple independent transitions in SWS1 copy number in the marine Hydrophis clade, with at least three lineages having multiple intact SWS1 genes: the previously studied Hydrophis cyanocinctus and at least two close relatives of this species; Hydrophis atriceps and Hydrophis fasciatus; and an individual Hydrophis curtus. In each lineage, gene copy divergence at a key spectral tuning site resulted in distinct UV and Violet/Blue-sensitive SWS1 subtypes. Both spectral variants were simultaneously expressed in the retinae of H. cyanocinctus and H. atriceps, providing the first evidence that these SWS1 expansions confer novel phenotypes. Finally, chromosome annotation for nine species revealed shared structural features in proximity to SWS1 regardless of copy number. If these features are associated with SWS1 duplication, expanded opsin complements could be more common in snakes than is currently recognized. Alternatively, selection pressures specific to aquatic environments could favor improved chromatic distinction in just some lineages.
Build-A-Genome and the “awesome power of undergraduates”
Authors: Boeke Jef D ,   the Build-A-Genome Course, Bader Joel S , Basta Leighanne , Cai Yizhi , Chapman Carolyn , Cooper Eric , Dymond Jessica , Han Jeffrey , Jones Richard M , Lauer Stephanie , Li Bing-Zhi , Mathews Debra , Matinyan Nick , Muller Héloïse , Newman Robert , Ordoñez Ciriza Raquel , Payea Matthew , Qu Amanda , Sandmeier Franziska , Scheifele Lisa , Sikder Hashmat , Yuan Yingjin , Zeller Karen , Zhao Yu 
Published: July 2024

Abstract
The Elizabeth W. Jones Award for Excellence in Education recognizes individuals or groups who have had significant, sustained impact on genetics education at any level, from K-12 through graduate school and beyond. The 2024 Elizabeth W. Jones Award for Excellence in Education recipient Jef Boeke considers himself a geneticist turned engineer. He transformed his landmark synthetic yeast genome project into a research-heavy teaching course, revolutionizing molecular biology and genetics education.
The Build-A-Genome course was developed to teach students basic practical molecular genetics while also providing the raw materials for a global genome synthesis project, Yeast 2.0. The course evolved over two decades to reflect the changing needs and opportunities for the project and the development of new technologies. In addition to educating a generation of college and high school students in a new way, it also developed a cadre of educators who developed similar courses and projects at a wide variety of research and educational institutions.
The Drosophila tumor necrosis factor Eiger promotes Myc supercompetition independent of canonical Jun N-terminal kinase signaling
Authors: Kodra Albana L , Singh Aditi Sharma , de la Cova Claire , Ziosi Marcello , Johnston Laura A 
Published: July 2024

Abstract
Numerous factors have been implicated in the cell–cell interactions that lead to elimination of cells via cell competition, a context-dependent process of cell selection in somatic tissues that is based on comparisons of cellular fitness. Here, we use a series of genetic tests in Drosophila to explore the relative contribution of the pleiotropic cytokine tumor necrosis factor α (TNFα) in Myc-mediated cell competition (also known as Myc supercompetition or Myc cell competition). We find that the sole Drosophila TNF, Eiger (Egr), its receptor Grindelwald (Grnd/TNF receptor), and the adaptor proteins Traf4 and Traf6 are required to eliminate wild-type “loser” cells during Myc cell competition. Although typically the interaction between Egr and Grnd leads to cell death by activating the intracellular Jun N-terminal kinase (JNK) stress signaling pathway, our experiments reveal that many components of canonical JNK signaling are dispensable for cell death in Myc cell competition, including the JNKKK Tak1, the JNKK Hemipterous and the JNK Basket. Our results suggest that Egr/Grnd signaling participates in Myc cell competition but functions in a role that is largely independent of the JNK signaling pathway.
Inter domain linker region affects properties of CBM6 in GH5_34 arabinoxylanases and alters oligosaccharide product profile
Authors: Norlander Siri , Jasilionis Andrius , Allahgholi Leila , Wennerberg Christina , Grey Carl , Adlercreutz Patrick , Karlsson Eva Nordberg 
Published: July 2024

Abstract
Understanding the relation between enzyme domain structure and catalytic activity is crucial for optimal engineering of novel enzymes for lignocellulose bioconversion. Xylanases with varying specificities are commonly used to valorise the hemicellulose arabinoxylan (AX), yet characterization of specific arabinoxylanases remain limited. Two homologous GH5_34 arabinoxylanases, HhXyn5A and CtXyn5A, in which the two domains are connected by a 40-residue linker, exhibit distinct activity on AX, yielding different reaction product patterns, despite high sequence identity, conserved active sites and similar domain composition. In this study, the carbohydrate binding module 6 (CBM6), or the inter domain linker together with CBM6, were swapped to investigate their influence on hydrolytic activity and oligosaccharide product pattern on cereal AXs. The variants, with only CBM6 swapped, displayed reduced activity on commercial wheat and rye AX, as well as on extracted oat fibre, compared to the original enzymes. Additionally, exchange of both linker and CBM6 resulted in a reduced ratio of enzyme produced in soluble form in Escherichia coli cultivations, causing loss of activity of both HhXyn5A and CtXyn5A variants. Analysis of oligosaccharide product patterns applying HPAEC–PAD revealed a decreased number of reaction products for CtXyn5A with swapped CBM6, which resembled the product pattern of HhXyn5A. These findings emphasize the importance of the CBM6 interactions with the linker and the catalytic domain for enzyme activity and specificity, and underlines the role of the linker in enzyme structure organisation and product formation, where alterations in linker interactions with the catalytic and/or CBM6 domains, influence enzyme-substrate association and specificity.
Dynamic temporal transcriptome analysis reveals grape VlMYB59-VlCKX4 regulatory module controls fruit set
Authors: Shi Qiaofang , Li Xufei , Yang Shengdi , Zhao Xiaochun , Yue Yihan , Yang Yingjun , Yu Yihe 
Published: July 2024

Abstract
Fruit set is a key stage in determining yield potential and guaranteeing quality formation and regulation. N-(2-chloro-4-pyridyl)-N′-phenylurea (CPPU) has been widely applied in grape production, the most iconic of which is the promotion of grape fruit set. However, current studies still lack the molecular mechanism of CPPU-induced grape fruit set. Here, the dynamic, high-resolution stage-specific transcriptome profiles were generated based on two different treatments and five developmental periods during fruit set in ‘Kyoho’ grape (Vitis vinifera L. × V. labrusca L.). Pairwise comparison and functional category analysis showed that phytohormone action cytokinin was significantly enriched during the CPPU-induced grape fruit set, but not the natural one. Value differentially expressed gene (VDEG) was a newly proposed analysis strategy for mining genes related to the grape fruit set. Notably, the cytokinin metabolic process was significantly enriched among up-regulated VDEGs. Of importance, a key VDEG VlCKX4 related to the cytokinin metabolic process was identified as related to the grape fruit set. Overexpression of VlCKX4 gene promoted the Arabidopsis plants that produce more and heavier siliques. The transcription factor VlMYB59 directly bound to the promoter of VlCKX4 and activated its expression. Moreover, overexpression of VlMYB59 gene also promoted the Arabidopsis fruit set. Overall, VlMYB59 responded to CPPU treatment and directly activated the expression of VlCKX4, thus promoting the fruit set. A regulatory pathway of the VlMYB59-VlCKX4 module in the fruit set was uncovered, which provides important insights into the molecular mechanisms of the fruit set and good genetic resources for high fruit set rate breeding.
The gap-free genome of Forsythia suspensa illuminates the intricate landscape of centromeres
Authors: Cui Jian , Zhu Congle , Shen Lisha , Yi Congyang , Wu Rong , Sun Xiaoyang , Han Fangpu , Li Yong , Liu Yang 
Published: July 2024

Abstract
Forsythia suspensa, commonly known as weeping forsythia, holds significance in traditional medicine and horticulture. Despite its ecological and cultural importance, the existing reference genome presents challenges with duplications and gaps, hindering in-depth genomic analyses. Here, we present a Telomere-to-Telomere (T2T) assembly of the F. suspensa genome, integrating Oxford Nanopore Technologies (ONT) ultra-long, Hi-C datasets, and high-fidelity (HiFi) sequencing data. The T2T reference genome (Fsus-CHAU) consists of 14 chromosomes, totaling 688.79 Mb, and encompasses 33 932 predicted protein-coding genes. Additionally, we characterize functional centromeres in the F. suspensa genome by developing a specific CENH3 antibody. We demonstrate that centromeric regions in F. suspensa exhibit a diverse array of satellites, showcasing distinctive types with unconventional lengths across various chromosomes. This discovery offers implications for the adaptability of CENH3 and the potential influence on centromere dynamics. Furthermore, after assessing the insertion time of full-length LTRs within centromeric regions, we found that they are older compared to those across the entire genome, contrasting with observations in other species where centromeric retrotransposons are typically young. We hypothesize that asexual reproduction may impact retrotransposon dynamics, influencing centromere evolution. In conclusion, our T2T assembly of the F. suspensa genome, accompanied by detailed genomic annotations and centromere analysis, significantly enhances F. suspensa potential as a subject of study in fields ranging from ecology and horticulture to traditional medicine.
Treatment of Active Crohn’s Disease With Exclusive Enteral Nutrition Diminishes the Immunostimulatory Potential of Fecal Microbial Products
Authors: Kerbiriou Caroline , Dickson Caitlin , Nichols Ben , Logan Michael , Mascellani Anna , Havlik Jaroslav , Russell Richard K , Hansen Richard , Milling Simon , Gerasimidis Konstantinos 
Published: July 2024

Abstract

Background
Exclusive enteral nutrition (EEN) is an effective treatment for active Crohn’s disease (CD). This study explored the immunostimulatory potential of a cell-free fecal filtrate and related this with changes in the fecal microbiota and metabolites in children with active CD undertaking treatment with EEN.

Methods
Production of tumor necrosis factor α (TNFα) from peripheral blood mononuclear cells was measured following their stimulation with cell-free fecal slurries from children with CD, before, during, and at completion of EEN. The metabolomic profile of the feces used was quantified using proton nuclear magnetic resonance and their microbiota composition with 16S ribosomal RNA sequencing.

Results
Following treatment with EEN, 8 (72%) of 11 patients demonstrated a reduction in fecal calprotectin (FC) &gt;50% and were subsequently labeled FC responders. In this subgroup, TNFα production from peripheral blood mononuclear cells was reduced during EEN (P = .008) and reached levels like healthy control subjects. In parallel to these changes, the fecal concentrations of acetate, butyrate, propionate, choline, and uracil significantly decreased in FC responders, and p-cresol significantly increased. At EEN completion, TNFα production from peripheral blood mononuclear cells was positively correlated with butyrate (rho = 0.70; P = .016). Microbiota structure (β diversity) was influenced by EEN treatment, and a total of 28 microbial taxa changed significantly in fecal calprotectin responders. At EEN completion, TNFα production positively correlated with the abundance of fiber fermenters from Lachnospiraceae_UCG-004 and Faecalibacterium prausnitzii and negatively with Hungatella and Eisenbergiella tayi.

Conclusions
This study offers proof-of concept data to suggest that the efficacy of EEN may result from modulation of diet-dependent microbes and their products that cause inflammation in patients with CD.
CRISPR/Cas9 Protocols for Disrupting Gene Function in the Non-vertebrate Chordate Ciona
Authors: Popsuj Sydney , Cohen Lindsey , Ward Sydney , Lewis Arabella , Yoshida Sean , Herrera R  Antonio , Cota Christina D , Stolfi Alberto 
Published: July 2024

Synopsis
The evolutionary origins of chordates and their diversification into the three major subphyla of tunicates, vertebrates, and cephalochordates pose myriad questions about the genetic and developmental mechanisms underlying this radiation. Studies in non-vertebrate chordates have refined our model of what the ancestral chordate may have looked like, and have revealed the pre-vertebrate origins of key cellular and developmental traits. Work in the major tunicate laboratory model Ciona has benefitted greatly from the emergence of CRISPR/Cas9 techniques for targeted gene disruption. Here we review some of the important findings made possible by CRISPR in Ciona, and present our latest protocols and recommended practices for plasmid-based, tissue-specific CRISPR/Cas9-mediated mutagenesis.
Defined synthetic microbial communities colonize and benefit field-grown sorghum
Authors: Fonseca-García Citlali , Pettinga Dean , Wilson Andrew , Elmore Joshua R , McClure Ryan , Atim Jackie , Pedraza Julie , Hutmacher Robert , Turumtay Halbay , Tian Yang , Eudes Aymerick , Scheller Henrik V , Egbert Robert G , Coleman-Derr Devin 
Published: July 2024

Abstract
The rhizosphere constitutes a dynamic interface between plant hosts and their associated microbial communities. Despite the acknowledged potential for enhancing plant fitness by manipulating the rhizosphere, the engineering of the rhizosphere microbiome through inoculation has posed significant challenges. These challenges are thought to arise from the competitive microbial ecosystem where introduced microbes must survive, and the absence of adaptation to the specific metabolic and environmental demands of the rhizosphere. Here, we engineered a synthetic rhizosphere community (SRC1) with the anticipation that it would exhibit a selective advantage in colonizing the host Sorghum bicolor, thereby potentially fostering its growth. SRC1 was assembled from bacterial isolates identified either for their potential role in community cohesion through network analysis or for their ability to benefit from host-specific exudate compounds. The growth performance of SRC1 was assessed in vitro on solid media, in planta under gnotobiotic laboratory conditions, and in the field. Our findings reveal that SRC1 cohesion is most robust when cultivated in the presence of the plant host under laboratory conditions, with lineages being lost from the community when grown either in vitro or in a native field setting. We establish that SRC1 effectively promotes the growth of both above- and below-ground plant phenotypes in both laboratory and native field contexts. Furthermore, in laboratory conditions, these growth enhancements correlate with the transcriptional dampening of lignin biosynthesis in the host. Collectively, these results underscore the potential utility of synthetic microbial communities for modulating crop performance in controlled and native environments alike.
Effects of artificial light on foraging behavior of the Pacific Kangaroo Rat (Dipodomys agilis)
Authors: Berry Kaitlyn E , Stapp Paul 
Published: July 2024

Abstract
Artificial light at night is increasingly recognized as a cause of habitat degradation, and as a conservation threat to wildlife species. We studied the behavioral response of Pacific kangaroo rats (Dipodomys agilis) to natural and artificial light in coastal sage scrub in southern California, United States. We used digital trail cameras to monitor visits to seed trays in shrub and open, intershrub microhabitats. Under natural-light conditions, kangaroo rats were more active on full- than new-moon nights, and concentrated foraging beneath shrubs. Surprisingly, kangaroo rats frequently interacted with other rodents in seed trays. Near to an artificial light source, kangaroo rats removed fewer seeds, had fewer foraging bouts, and spent less time in trays—especially in brightly lit open microhabitats—compared to distances farther from the light. Differences between the first and second nights of trials during both experiments suggested that kangaroo rats learned locations of resource-rich seed trays and modified their behavior accordingly. Our results are similar to recent studies showing that artificial light depresses foraging activity of rodents in the areas of highest illumination, and adds to evidence of the need to mitigate impacts of urban lighting in fragments of coastal sage scrub, especially along the urban–wildland interface.