bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plastomes of Garcinia mangostana L. and comparative analysis with other Garcinia species
Authors: Wee Ching-Ching , Nor Muhammad Nor Azlan , Subbiah Vijay Kumar , Arita Masanori , Nakamura Yasukazu , Goh Hoe-Han 
Published: February 2022

AbstractThe two varieties of mangosteen (Garcinia mangostana L.) cultivated in Malaysia are known as Manggis and Mesta. The latter is preferred for its flavor, texture, and seedlessness. Here, we report a complete plastome (156,580 bp) of the Mesta variety which was obtained through a hybrid assembly approach using PacBio and Illumina sequencing reads. It encompasses a large single-copy (LSC) region (85,383 bp) and a small single-copy (SSC) region (17,137 bp) that are separated by 27,230 bp of inverted repeat (IR) regions at both ends. The plastome comprises 128 genes, namely 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The plastome of the Manggis variety (156,582 bp) obtained from reference-guided assembly of Illumina reads was found to be nearly identical to Mesta except for two indels and the presence of a single nucleotide polymorphism (SNP). Comparative analyses with other publicly available Garcinia plastomes, including G. anomala, G. gummi-gutta, G. mangostana var. Thailand, G. oblongifolia, G. paucinervis, and G. pedunculata found that the gene content, gene order, and gene orientation were highly conserved among the Garcinia species. Phylogenomic analysis divided the six Garcinia plastomes into three groups with the Mesta and Manggis varieties clustered closer to G. anomala, G. gummi-gutta, and G. oblongifolia, while the Thailand variety clustered with G. pedunculata in another group. These findings serve as future references for the identification of species or varieties and facilitate phylogenomic analysis of lineages from the Garcinia genus to better understand their evolutionary history.
An expanded population of CD8dimT cells with features of mitochondrial dysfunction and senescence is associated with persistent HIV-associated Kaposi’s sarcoma under ART
Authors: Clutton Genevieve T , Weideman Ann Marie K , Goonetilleke Nilu P , Maurer Toby 
Published: February 2022

AbstractHIV-associated Kaposi’s sarcoma (KS), which is caused by Kaposi’s sarcoma-associated herpesvirus, usually arises in the context of uncontrolled HIV replication and immunosuppression. However, disease occasionally persists in individuals with durable HIV viral suppression and CD4 T cell recovery under anti-retroviral therapy (ART). The underlying mechanisms associated with this persistence are unclear. Suppression of viral infections can be mediated by CD8 T cells that detect infected cells via their T cell receptor and the CD8 co-receptor. However, CD8 T cells exhibit signs of functional exhaustion in untreated HIV infection that may not be fully reversed under ART. To investigate whether persistent KS under ART was associated with phenotypic and functional perturbations of CD8 T cells, we performed a cross-sectional study comparing HIV-infected individuals with persistent KS under effective ART (HIV+ KS+) to HIV-infected individuals receiving effective ART with no documented history of KS (HIV+ KSneg). A subset of T cells with low cell surface expression of CD8 (“CD8dimT cells”) was expanded in HIV+ KS+ compared with HIV+ KSnegparticipants. Relative to CD8brightT cells, CD8dimT cells exhibited signs of senescence (CD57) and mitochondrial perturbations (PGC-1α, MitoTracker) ex vivo. Mitochondrial activity (MitoTracker) was also reduced in proliferating CD8dimT cells. These findings indicate that an expanded CD8dimT cell population displaying features of senescence and mitochondrial dysfunction is associated with KS persistence under ART. CD8 co-receptor down-modulation may be symptomatic of ongoing disease.
Adverse effects of antipsychotic drugs on metabolism depend on drug dosing and feeding times
Authors: Zapata Rizaldy C , Silver Allison , Yoon Dongmin , Chaudry Besma , Libster Avraham , McCarthy Michael J , Osborn Olivia 
Published: February 2022

AbstractAntipsychotic drugs (AP) are highly efficacious treatments for psychiatric disorders but are associated with significant metabolic side effects. The circadian clock maintains metabolic homeostasis by sustaining daily rhythms in feeding, fasting and hormone regulation but how circadian rhythms interact with AP and its associated metabolic side effects is not well known. In these studies, we investigated the impact of time of AP dosing on the development of metabolic side effects. In mice, AP dosing at the start of the light cycle (AM) resulted in significant increase in food intake, weight gain compared with equivalent dose before the onset of darkness (PM). Time of AP dosing also impacted circadian gene expression, metabolic hormones and inflammatory pathways and their diurnal expression patterns. To examine the possibility of time-dependent AP effects in humans, we conducted a retrospective examination of weight and metabolic outcomes in patients who received risperidone (RIS) for the treatment of serious mental illness. Using pharmacy records to estimate the time of RIS dosing, we observed a significant association between time of dosing and severity of RIS-induced metabolic side effects. Eating within a restricted time window (Time restricted feeding/eating, TRF/TRE) has been shown in both mouse and human studies to be an effective therapeutic intervention against obesity and metabolic disease. We demonstrate, for the first time, that TRF is an effective intervention to reduce AP-induced metabolic side effects in mice. These studies identify highly effective and translatable interventions to mitigate AP-induced metabolic side effects.
Fourth Wave of COVID-19 in India : Statistical Forecasting
Authors: Rajeshbhai Sabara Parshad , Dhar Subhra Sankar , Shalabh  
Published: February 2022

AbstractThe spread of COVID-19 pandemic has wave nature. This article proposes a statistical methodology to study and forecast the future waves. The methodology is applied to COVID-19 data from India to statistically forecast the occurrence of fourth wave in India. In the course of this study, the data is fitted by the mixture of Gaussian distribution, and Bootstrap methodology is used to compute the confidence interval of the time point of peak of the fourth wave. This methodology can also be used to forecast the fourth and other waves in other countries also.
Challenges and Opportunities Experienced by Performing Artists during COVID-19 Lockdown: Scoping Review
Authors: Brooks Samantha K , Patel Sonny S 
Published: February 2022

AbstractThis scoping review synthesises published literature on the experiences of professional and amateur performing artists during COVID-19 and their perceptions of the challenges and opportunities faced. Six electronic databases were searched for published English-language articles containing primary data on this topic; twenty-one studies were reviewed. Themes included loss of work, financial impact, concerns about the future, psychological wellbeing, social connections, continuing creative pursuits, and inequalities. Participants reported both detrimental psychological effects of lockdown such as anxiety and sleep problems and positive effects including reduced stress and enjoyment of having more free time. Most continued creative pursuits throughout lockdown, most commonly shifting to online platforms. However, many barriers to creative pursuits were reported, including lack of technological expertise or equipment. Concerns were raised about inequality, in particular racial disparities in the financial impact of the pandemic and additional pressures faced by performers with disabilities; with insufficient funds to afford the equipment needed to shift to remote performing; and with additional caring responsibilities. It is important that performing artists have access to peer support; that education on digital technologies is incorporated into future performing arts education; and that inequities are addressed to ensure the needs of diverse communities are met.
Mitochondrial Genome of Garcinia mangostana L. variety Mesta
Authors: Wee Ching-Ching , Nor Muhammad Nor Azlan , Subbiah Vijay Kumar , Arita Masanori , Nakamura Yasukazu , Goh Hoe-Han 
Published: February 2022

AbstractFruits of Garcinia mangostana L. (mangosteen) are rich in nutrients with xanthones found in the pericarp having great pharmaceutical potential. Mangosteen variety Mesta is only found in Malaysia, which tastes sweeter than the common Manggis variety in Southeast Asia. In this study, we report the complete mitogenome of G. mangostana L. variety Mesta with a total sequence length of 371,235 bp of which 1.7% could be of plastid origin. The overall GC content of the mitogenome is 43.8%, comprising 29 protein-coding genes, 3 rRNA genes, and 21 tRNA genes. Repeat and tandem repeat sequences accounted for 5.8% and 0.15% of the Mesta mitogenome, respectively. There are 333 predicted RNA-editing sites in Mesta mitogenome. These include the RNA-editing events that generated the start codon of nad1 gene and the stop codon of ccmFC gene. Phylogenomic analysis with a maximum likelihood method showed that the mitogenome of mangosteen variety Mesta was grouped under Malpighiales order. This is the first complete mitogenome from the Garcinia genus for future evolutionary studies.
Arabidopsis histone H3 lysine 9 methyltransferases KYP/SUVH5/6 are involved in leaf development by interacting with AS1-AS2 to repress KNAT1 and KNAT2
Authors: Hung Fu-Yu , Feng Yun-Ru , Shih Yuan-Hsin , Lai You-Cheng , Wu Keqiang 
Published: February 2022

AbstractArabidopsis KRYPTONITE/SUPPRESSOR OF VARIEGATION 3–9 HOMOLOG 4 (KYP/SUVH4), SUVH5 and SUVH6 are H3K9 methyltransferases and they are redundantly involved in silencing of transposable elements (TEs). A recent study indicated that KYP/SUVH5/6 can directly interact with the histone deacetylase HDA6 to synergistically regulate TE expression. However, the function of KYP/SUVH5/6 in plant development is still unclear. The ASYMMETRIC LEAVES1 (AS1) and AS2 form a transcription complex, which is involved in leaf development by repressing the homeobox genes KNOTTED-LIKE FROM ARABIDOPSIS THALIANA 1 (KNAT1) and KNAT2. In this study, we found that KYP and SUVH5/6 directly interact with AS1-AS2 to repress KNAT1 and KNAT2 by altering histone H3 acetylation and H3K9 dimethylation levels. In addition, KYP can directly target on the promoters of KNAT1 and KNAT2, and the binding of KYP is dependent on AS1. Furthermore, the genome-wide occupancy profile of KYP indicated that KYP is enriched in the promoter regions of coding genes, and the binding of KYP is positively correlated with that of AS1 and HDA6. Together, these results indicate that Arabidopsis H3K9 methyltransferases KYP/SUVH5/6 are involved in leaf development by interacting with AS1-AS2 to alter histone H3 acetylation and H3K9 dimethylation from the KNAT1 and KNAT2 loci.
Bacterial metatranscriptomes in wastewater can differentiate virally infected human populations
Authors: Salido Rodolfo A , Martino Cameron , Karthikeyan Smruthi , Huang Shi , Rahman Gibraan , Gonzalez Antonio , Zaramela Livia S. , Beck Kristen L , Bhute Shrikant , Cantrell Kalen , Carrieri Anna Paola , Farmer Sawyer , Haiminen Niina , Humphrey Greg , Kim Ho-Cheol , Parida Laxmi , Richter Alex , Vázquez-Baeza Yoshiki , Zengler Karsten , Swafford Austin D. , Bartko Andrew , Knight Rob 
Published: February 2022

AbstractMonitoring wastewater samples at building-level resolution screens large populations for SARS-CoV-2, prioritizing testing and isolation efforts. Here we perform untargeted metatranscriptomics on virally-enriched wastewater samples from 10 locations on the UC San Diego campus, demonstrating that resulting bacterial taxonomic and functional profiles discriminate SARS-CoV-2 status even without direct detection of viral transcripts. Our proof-of-principle reveals emergent threats through changes in the human microbiome, suggesting new approaches for untargeted wastewater-based epidemiology.
ΔNp63 drives dysplastic alveolar remodeling and restricts epithelial plasticity upon severe lung injury
Authors: Weiner Aaron I. , Zhao Gan , Zayas Hanna M. , Holcomb Nicolas P. , Adams-Tzivelekidis Stephanie , Wong Joanna , Gentile Maria E. , Palashikar Gargi , Quansah Kwaku , Vaughan Andrew E. 
Published: February 2022

AbstractUnlike many mammalian vital organs, the lung exhibits a robust, multifaceted regenerative response to severe injuries such as influenza infection, which primarily targets epithelial cells in the airways and alveoli. Quiescent lung-resident epithelial progenitors proliferate, migrate, and differentiate following lung injury, participating in two distinct reparative pathways: functionally beneficial regeneration and dysplastic tissue remodeling. Intrapulmonary airway-resident basal-like p63+progenitors are one such progenitor cell type that migrates from the airways to form ectopic bronchiolar tissue in the alveoli, generating honeycomb-like cysts that fail to resolve after injury. Though this phenomenon is now well described, the cell-autonomous signals that drive dysplastic alveolar remodeling remain uncertain, a question made especially salient by observations that p63+progenitors also expand dramatically upon diffuse alveolar damage in humans resulting from a variety of insults including SARS-CoV-2-induced ARDS. Here we show that the master basal cell transcription factor ΔNp63 is required for the immense migratory capacity of intrapulmonary p63+progenitors and consequently for the dysplastic repair pathway manifest by these cells. We further demonstrate that ΔNp63 restricts the fate plasticity of intrapulmonary p63+progenitors by regulating their epigenetic landscape, and that loss of ΔNp63 alters the deposition of active and repressive histone modifications at key differentiation gene loci, allowing ΔNp63KOprogenitors to proceed towards airway or alveolar differentiation depending on their surrounding environment. These insights into the regulatory mechanisms of dysplastic repair and intrapulmonary p63+progenitor fate choice highlight potential therapeutic targets to promote more effective alveolar regeneration following severe lung injuries.
Prediction of sex-determination mechanisms in avian primordial germ cells using RNA-seq analysis
Authors: Ichikawa Kennosuke , Nakamura Yoshiaki , Bono Hidemasa , Ezaki Ryo , Matsuzaki Mei , Horiuchi Hiroyuki 
Published: February 2022

AbstractAvian sex is determined by various factors, such as the dosage of DMRT1 and cell-autonomous mechanisms. While the sex-determination mechanism in gonads is well analyzed, the mechanism in germ cells remains unclear. In this study, we explored the gene expression profiles of male and female primordial germ cells (PGCs) during embryogenesis in chickens to predict the mechanism of sex-determination. Male and female PGCs were isolated from blood and gonads with a purity > 96% using flow cytometry and analyzed using RNA-seq. Prior to settlement in the gonads, female circulating PGCs (cPGCs) obtained from blood displayed sex-biased expression. Gonadal PGCs (gPGCs) also displayed sex-biased expression, and the number of female-biased genes detected was higher than male-biased genes. The female-biased genes in gPGCs were enriched in some metabolic processes. To reveal the mechanisms underlying the transcriptional regulation of female-biased genes in gPGCs, we performed stimulation tests. Stimulation with retinoic acid against cultured gPGCs derived from male embryos resulted in the upregulation of several female-biased genes. Overall, our results suggest that sex determination of avian PGCs possess aspects of both cell-autonomous and somatic cell regulation. Moreover, it appears that sex determination occurs earlier in females than in males.
Cryo-electron tomography of Birbeck granules reveals the molecular mechanism of langerin lattice formation
Authors: Oda Toshiyuki , Yanagisawa Haruaki , Shinmori Hideyuki , Ogawa Youichi , Kawamura Tatsuyoshi 
Published: February 2022

AbstractLangerhans cells are specialized antigen-presenting cells localized within the epidermis and mucosal epithelium. Upon contact with Langerhans cells, pathogens are captured by the C- type lectin langerin and internalized into a structurally unique vesicle known as a Birbeck granule. Although the immunological role of Langerhans cells and Birbeck granules have been extensively studied, the mechanism by which the characteristic zippered membrane structure of Birbeck granules is formed remains elusive. In this study, we observed isolated Birbeck granules using cryo-electron tomography and reconstructed the 3D structure of the repeating unit of the honeycomb lattice of langerin at 6.4 Å resolution. We found that the interaction between the two langerin trimers was mediated by docking the flexible loop at residues 258-263 into the secondary carbohydrate-binding cleft. Mutations within the loop inhibited Birbeck granule formation and the internalization of HIV pseudovirus. These findings suggest a molecular mechanism for membrane zippering during Birbeck granule biogenesis and provide insight into the role of langerin in the defense against viral infection.
Metabolic Engineering of Oleaginous Yeast Rhodotorula toruloides for Overproduction of Triacetic Acid Lactone
Authors: Cao Mingfeng , Tran Vinh G. , Qin Jiansong , Olson Andrew , Schultz J. Carl , Huang Chunshuai , Xie Dongming , Zhao Huimin 
Published: February 2022

AbstractThe plant-sourced polyketide triacetic acid lactone (TAL) has been recognized as a promising platform chemical for the biorefinery industry. However, its practical application was rather limited due to low natural abundance and inefficient cell factories for biosynthesis. Here we report the metabolic engineering of oleaginous yeast Rhodotorula toruloides for TAL overproduction. We first introduced a 2-pyrone synthase gene from Gerbera hybrida (GhPS) into R. toruloides and investigated the effects of different carbon sources on TAL production. We then systematically employed a variety of metabolic engineering strategies to increase the flux of acetyl-CoA by enhancing its biosynthetic pathways and disrupting its competing pathways. We found that overexpression of citrate lyase (ACL1) improved TAL production by 45% compared to the GhPS overexpressing strain, and additional overexpression of acetyl-CoA carboxylase (ACC1) further increased TAL production by 29%. Finally, we characterized the resulting strain I12-ACL1-ACC1 using fed-batch bioreactor fermentation in glucose or oilcane juice medium with acetate supplementation and achieved a titer of 28 g/L or 23 g/L TAL, respectively. This study demonstrates that R. toruloides is a promising host for production of TAL and other acetyl-CoA-derived polyketides from low-cost carbon sources.Graphical abstractTriacetic acid lactone (TAL) is a promising platform chemical. Cao et al. overexpressed 2-pyrone synthase in oleaginous yeast Rhodotorula toruloides to produce TAL. They systematically evaluated various metabolic gene targets to increase acetyl-CoA and malonyl-CoA levels for TAL production and found that overexpression of both ACL1 and ACC1 led to 28 g/L or 23 g/L of TAL from glucose or oilcane juice with acetate supplementation, respectively, in fed-batch fermentation.
Multiple scenarios for sexual crosses in the fungal pathogen Zymoseptoria tritici on wheat residues: potential consequences for virulence gene transmission
Authors: Orellana-Torrejon Carolina , Vidal Tiphaine , Gazeau Gwilherm , Boixel Anne-Lise , Gélisse Sandrine , Lageyre Jérôme , Saint-Jean Sébastien , Suffert Frédéric 
Published: February 2022

AbstractLittle is known about the impact of host immunity on sexual reproduction in fungal pathogens. In particular, it is unclear whether crossing requires both sexual partners to infect living plant tissues. We addressed this issue in a three-year experiment investigating different scenarios of Zymoseptoria tritici crosses on wheat according to the virulence (‘vir’) or avirulence (‘avr’) of the parents against a qualitative resistance gene. Co-inoculations (‘vir × vir’, ‘avr × vir’, ‘avr × avr’) and single inoculations were performed on a cultivar carrying the resistance gene (Cellule) and a susceptible cultivar (Apache), in the greenhouse. We assessed the intensity of asexual multiplication by scoring disease severity, and the intensity of sexual reproduction by counting the ascospores discharged from wheat residues. As expected, disease severity was more intense on Cellule for ‘vir × vir’ co-inoculations than for ‘avr × vir’ co-inoculations, with no disease for ‘avr × avr’. However, all types of co-inoculation yielded sexual offspring, whether or not the parental strains caused plant symptoms. Parenthood was confirmed by genotyping (SSR markers), and the occurrence of crosses between (co-)inoculated and exogenous strains (other strains from the experiment, or from far away) was determined. We found that symptomatic asexual infection was not required for a strain to participate in sexual reproduction, and that avirulent strains could be maintained asymptomatically “on” or “in” leaf tissues of plants carrying the corresponding resistant gene for long enough to reproduce sexually. In two of the three years, the intensity of sexual reproduction did not differ significantly between the three types of co-inoculation in Cellule, suggesting that crosses involving avirulent strains are not anecdotal. We discuss the possible mechanisms explaining the maintenance of avirulence in Z. tritici populations and supporting the potential efficacy of cultivar mixtures for limiting resistance gene breakdown.HighlightsAvirulent Zymoseptoria tritici strains can reproduce sexually in wheat plants carrying the corresponding resistant gene.Symptomatic infection of plant tissues is not essential for a strain to reproduce sexually.Avirulent strains can be maintained asymptomatically “on” or “in” leaf tissues of plants carrying the corresponding resistant gene for long enough to reproduce sexually.Crosses of virulent strains with virulent and avirulent strains in a plant host carrying the corresponding resistance gene can produce offspring with similar population sizes.Several possible scenarios for sexual crosses can explain the maintenance of avirulence in Zymoseptoria tritici populations evolving in a wheat canopy, particular in cultivar mixtures.
An Agrobacterium strain auxotrophic for methionine is useful for switchgrass transformation
Authors: Prías-Blanco Mónica , Chappell Timothy M. , Freed Emily F. , Illa-Berenguer Eudald , Eckert Carrie A. , Parrott Wayne A. 
Published: February 2022

SummaryAuxotrophic strains of Agrobacterium tumefaciens can contribute to the development of more efficient transformation systems, especially for crops historically considered recalcitrant. Homologous recombination was used to derive methionine auxotrophs of two common A. tumefaciens strains, LBA4404 and EHA105. The EHA105 strains were more efficient for switchgrass transformation, while both the EHA105 and LBA4404 strains worked equally well for the rice control. Event quality, as measured by transgene copy number, was not affected by auxotrophy, but was higher for the LBA4404 strains than the EHA105 strains. Ultimately, the use of auxotrophs reduced bacterial overgrowth during co-cultivation, with a concomitant decrease in the need for antibiotics. In turn, reduced overgrowth allowed longer co-cultivation periods, with a trend towards higher transformation frequencies for switchgrass, but not for rice.