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Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Journal of Integrative Plant Biology 2024年第3期66卷 546-578页

作者： Guojin Zhang Hong Ma College of Life Sciences Hunan Normal UniversityChangsha 410081China Department of Biology 510 Mueller LaboratoryHuck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPA 16802USA

Angiosperms(flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the “abominable mystery,”hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological,and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences,dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families,and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella,Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and ***, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore,we discuss the implicatio

关键词： angiosperms evolution flowering plants nuclear gene phylogenomics phylogeny

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Angiosperm-wide analysis of fruit and ovary evolution aided by a new nuclear phylogeny supports association of the same ovary type with both dry and fleshy fruits

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Journal of Integrative Plant Biology 2024年第2期66卷 228-251页

作者： Yezi Xiang Taikui Zhang Yiyong Zhao Hongjin Dong Hongyi Chen Yi Hu Chien-Hsun Huang Jun Xiang Hong Ma state Key Laboratory of Genetic Engineering Ministry of Education Key Laboratory of Biodiversity and Ecological EngineeringInstitute of Plant BiologyCenter of Evolutionary BiologySchool of Life SciencesFudan UniversityShanghai 200438China Department of Biology Howard Hughes Medical InstituteDuke UniversityDurhamNC 27708USA Department of Biology the Eberly College of Scienceand the Huck Institutes of the Life Sciencesthe Pennsylvania State UniversityUniversity ParkPA 16802USA Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization College of Biology and Agricultural ResourcesHuanggang Normal UniversityHuanggang 438000China

Fruit functions in seed protection and dispersal and belongs to many dry and fleshy types,yet their evolutionary pattern remains unclear in part due to uncertainties in the phylogenetic relationships among several orders and *** we used nuclear genes of 502 angiosperm species representing 231 families to reconstruct a well supported phylogeny,with resolved relationships for orders and families with previously uncertain *** this phylogeny as a framework,molecular dating supports a Triassic origin of the crown angiosperms,followed by the emergence of most orders in the Jurassic and Cretaceous and their rise to ecological dominance during the Cretaceous Terrestrial *** robust phylogeny allowed an examination of the evolutionary pattern of fruit and ovary types,revealing a trend of parallel carpel fusions during early diversifications in eudicots,monocots,and ***,taxa in the same order or family with the same ovary type can develop either dry or fleshy fruits with strong correlations between specific types of dry and fleshy fruits;such associations of ovary,dry and fleshy fruits define several ovaryfruit"modules"each found in multiple *** of the frequent modules has an ovary containing multiple ovules,capsules and berries,and another with an ovary having one or two ovules,achenes(or other single-seeded dry fruits)and *** new perspective of relationships among fruit types highlights the closeness of specific dry and fleshy fruit types,such as capsule and berry,that develop from the same ovary type and belong to the same module relative to dry and fleshy fruits of other modules(such as achenes and drupes).Further analyses of gene families containing known genes for ovary and fruit development identified phylogenetic nodes with multiple gene duplications,supporting a possible role of whole-genome duplications,in combination with climate changes and animal behaviors,in angiosperm fruit and ovary diversificat

关键词： angiosperm fruit evolution MADS-box molecular clock nuclear phylogeny ovary and fruit developmental genes

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Machine learning in concrete science:applications,challenges,and best practices

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npj Computational Materials 2022年第1期8卷 1192-1208页

作者： Zhanzhao Li Jinyoung Yoon Rui Zhang Farshad Rajabipour Wil V.Srubar III Ismaila Dabo Aleksandra Radlińska Department of Civil and Environmental Engineering The Pennsylvania State UniversityUniversity ParkPA16802USA Department of Structural Engineering Research Korea Institute of Civil Engineering and Building Technology(KICT)Goyang-si10223Republic of Korea Department of Civil Environmentaland Architectural EngineeringUniversity of Colorado BoulderBoulderCO80309USA Materials Science and Engineering Program University of Colorado BoulderBoulderCO80309USA Department of Materials Science and Engineering The Pennsylvania State UniversityUniversity ParkPA16802USA

Concrete,as the most widely used construction material,is inextricably connected with human *** conceptual and methodological progress in concrete science,concrete formulation for target properties remains a challenging task due to the ever-increasing complexity of cementitious *** the ability to tackle complex tasks autonomously,machine learning(ML)has demonstrated its transformative potential in concrete *** the rapid adoption of ML for concrete mixture design,there is a need to understand methodological limitations and formulate best practices in this emerging computational ***,we review the areas in which ML has positively impacted concrete science,followed by a comprehensive discussion of the implementation,application,and interpretation of ML *** conclude by outlining future directions for the concrete community to fully exploit the capabilities of ML models.

关键词： concrete directions autonomous

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Investigations on the Optimization of Contacts Barrier Height for the Improved Performance of ZnO/CdS/CZTS Solar Cells

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Energy Engineering 2023年第8期120卷 1803-1815页

作者： Fatiha Daoudi Abdelkrim Naas Omar Meglali Radia Boudaira Ahmed Gueddim A.M.Saeed Material Science and Informatics Laboratory University of DjelfaDjelfa17000Algeria Faculty of Sciences University of M’silaM’sila28000Algeria Department of Physics University of ConstantineConstantine25000Algeria Department of Physics Division of Science and TechnologyUniversity of EducationLahorePakistan

The numerical simulations were performed using the AMPS-1D simulator to study the effects of the CZTS as an absorber layer and the contacts’barrier height on the performance of four ZnO/CdS/CZTS solar *** obtain the best cell performances,the barrier heights of the back and front contacts were adjusted between 0.01,0.77,0.5,and 1.55 eV,*** simulations,we used the lifetime mode,and the device performances were evaluated under AM1.5 illumination *** found that the efficiency,fill factor,and open-circuit voltage were almost constant at a front contact barrier height of less than 0.31 *** short-current density was not affected by the front contact barrier *** back contact material had a significant impact on the CZTS cells *** best performance was obtained for the CZTS550 cell with JSC=29.53 mA/cm2,VOC=1.07 V,FF=0.88,andη=28.08%at barrier heights of 0.31 and 1.55 eV for front and back contacts,*** conduction band offset at the CZTS550/CdS hetero-junction was found to be spike-like with 0.21 *** obtained conversion efficiency is comparable to those previously reported in the literature.

关键词： CZTS solar cell barrier height AMPS-1D photovoltaic parameters

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Fabricating 3-dimensional human brown adipose microtissues for transplantation studies

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Bioactive Materials 2023年第4期22卷 518-534页

作者： Ou Wang Li Han Haishuang Lin Mingmei Tian Shuyang Zhang Bin Duan Soonkyu Chung Chi Zhang Xiaojun Lian Yong Wang Yuguo Lei Department of Chemical and Biomolecular Engineering University of Nebraska-LincolnNEUSA Biomedical Engineering Program University of Nebraska-LincolnNEUSA Department of Biomedical Engineering Pennsylvania State UniversityPAUSA China Novartis Institutes for BioMedical Research Co. Ltd.BeijingChina Department of Chemistry University of Nebraska-LincolnNEUSA Mary&Dick Holland Regenerative Medicine Program and Division of Cardiology Department of Internal MedicineUniversity of Nebraska Medical CenterOmahaNEUSA Department of Nutrition University of MassachusettsAmherstMAUSA School of Biological Science University of Nebraska-LincolnNEUSA Huck Institutes of the Life Sciences Pennsylvania State UniversityPAUSA

Transplanting cell cultured brown adipocytes(BAs)represents a promising approach to prevent and treat obesity(OB)and its associated metabolic disorders,including type 2 diabetes mellitus(T2DM).However,transplanted BAs have a very low survival rate in *** enzymatic dissociation during the harvest of fully differentiated BAs also loses significant *** is a critical need for novel methods that can avoid cell death during cell preparation,transplantation,and in ***,we reported that preparing BAs as injectable microtissues could overcome the *** found that 3D culture promoted BA differentiation and UCP-1 expression,and the optimal initial cell aggregate size was 100μ*** microtissues could be produced at large scales via 3D suspension assisted with a PEG hydrogel and could be *** microtissues could survive in vivo for long *** alleviated body weight and fat gain and improved glucose tolerance and insulin sensitivity in high-fat diet(HFD)-induced OB and T2DM *** microtissues impacted multiple organs,secreted protein factors,and influenced the secretion of endogenous *** our best knowledge,this is the first report on fabricating human BA microtissues and showing their safety and efficacy in T2DM *** proposal of transplanting fabricated BA microtissues,the microtissue fabrication method,and the demonstration of efficacy in T2DM mice are all *** results show that engineered 3D human BA microtissues have considerable advantages in product scalability,storage,purity,safety,dosage,survival,and efficacy.

关键词： Brown adipocyte Microtissue Transplantation Obesity Type 2 diabetes

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Comprehensive phylogenetic analyses of Orchidaceae using nuclear genes and evolutionary insights into epiphytism

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Journal of Integrative Plant Biology 2023年第5期65卷 1204-1225页

作者： Guojin Zhang Yi Hu Ming-Zhong Huang Wei-Chang Huang Ding-Kun Liu Diyang Zhang Haihua Hu Jason L.Downing Zhong-Jian Liu Hong Ma Department of Biology 510 Mueller LaboratoryHuck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPennsylvania 16802USA Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture Fujian Agriculture and Forestry UniversityFuzhou 350002China Shanghai Chenshan Botanical Garden SongjiangShanghai 201602China state Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China Fairchild Tropical Botanic Garden Coral GablesFlorida 33156USA

Orchidaceae(with>28,000 orchid species)are one of the two largest plant families,with economically and ecologically important species,and occupy global and diverse niches with primary distribution in *** orchids,70%grow on other plants as epiphytes;epiphytes contribute up to~50%of the plant diversity in rainforests and provide food and shelter for diverse animals and microbes,thereby contributing to the health of these *** account for over two-thirds of vascular epiphytes and provide an excellent model for studying evolution of *** phylogenetic studies of Orchidaceae and subgroups have;been crucial for understanding relationships among many orchid lineages,although some uncertainties *** example,in the largest subfamily Epidendroideae with nearly all epiphytic orchids,relationships among some tribes and many subtribes are still controversial,hampering evolutionary analyses of *** we obtained 1,450 low-copy nuclear genes from 610 orchid species,including 431 with newly generated transcriptomes,and used them for the reconstruction of robust Orchidaceae phylogenetic trees with highly supported placements of tribes and *** also provide generally wellsupported phylogenetic placements of 131 genera and 437 species that were not sampled by previous plastid and nuclear phylogenomic *** clock analyses estimated the Orchidaceae origin at~132 million years ago(Ma)and divergences of most subtribes from 52 to 29 *** reconstruction supports at least 14 parallel origins of epiphytism;one such origin was placed at the most recent common ancestor of~95%of epiphytic orchids and linked to modern *** occurrences of rapid increase in the diversification rate were detected within Epidendroideae near and after the K-Pg boundary,contributing to~80%of the Orchidaceae *** study provides a robust and the largest family-wide Orchidaceae nuclear phylogenetic tree thus far and

关键词： convergence epiphytes evolution orchids parallel rainforest phylogenomics transcriptome

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The influence of aspect ratio on the properties of cobalt nanowire-based magnetorheological fluids

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International Journal of Smart and Nano Materials 2022年第4期13卷 626-642页

作者： R.C Bell N.M Wereley Department of Chemistry The Pennsylvania State UniversityAltoona CollegeAltoonaPAUSA Department of Aerospace Engineering University of MarylandCollege ParkMdUSA

The yield stress of magnetorheological(MR)fluids has been shown to depend on particle morphology,but the exact nature of this contribution is still not fully *** this study,MR fluids containing 4 vol.%cobalt particles(spherical particles ***-wires)suspended in silicone oil were *** influence of the aspect ratio on the rheological properties of suspensions that contained cobalt nanowires with aspect ratios ranging from 10 to 101 in increments of~6 is *** cobalt nanowires were fabricated using alumina template-based electrodeposition,produ-cing wires with 305±66 nm *** shear stress was measured as a function of shear rate for increasing applied mag-netic *** apparent yield stress and viscosity as a function of changing aspect ratio of the nanowire suspensions were *** a saturated magnetic flux density,the yield stress was found to increase linearly up to an aspect ratio of 23(7.1μm long wires)at which time the yield stress reached a plateau of 3.7 kPa even as the aspect ratio was further *** a comparison,suspensions containing 4 vol.%1.6μm spherical cobalt particles only reached a maximum yield stress of 1.6 kPa.

关键词： Magnetorheological fluids nanowires size dependence

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Superior printed parts using history and augmented machine learning

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npj Computational Materials 2022年第1期8卷 1736-1745页

作者： Meng Jiang Tuhin Mukherjee Yang Du Tarasankar DebRoy state Key Laboratory of Advanced Welding and Joining Harbin Institute of TechnologyHarbin150001China Department of Materials Science and Engineering The Pennsylvania State UniversityUniversity ParkPA16802USA

Machine learning algorithms are a natural fit for printing fully dense superior metallic parts since 3D printing embodies digital technology like no other manufacturing *** traditional machine learning needs a large volume of reliable historical data to optimize many printing variables,the algorithm is augmented with human intelligence derived from the rich knowledge base of metallurgy and physics-based *** augmentation improves the computational efficiency and makes the problem tractable by enabling the algorithm to use a small set of *** provide a verifiable quantitative index for achieving fully dense superior parts,facilitate material selection,uncover the hierarchy of important variables that affect the density,and present easy-to-use visual process *** findings can improve the quality consistency of 3D printed parts that now limit their greater industrial *** approach used here can be applied to solve other problems of 3D printing and beyond.

关键词： printing augmented consistency

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A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C4 photosynthesis

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Molecular Plant 2022年第4期15卷 755-777页

作者： Weichen Huang Lin Zhang JTravis Columbus Yi Hu Yiyong Zhao Lin Tang Zhenhua Guo Wenli Chen Michael McKain Madelaine Bartlett Chien-Hsun Huang De-Zhu Li Song Ge Hong Ma Department of Biology 510 Mueller LaboratoryHuck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkState CollegePA 16802USA Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering and state Key Laboratory of Genetic Engineering Institute of Biodiversity Sciences and Institute of Plant BiologySchool of Life SciencesFudan University2005 Songhu RoadShanghai 200438China Rancho Santa Ana Botanic Garden and Claremont Graduate university 1500 North College AvenueClaremontCA 91711USA College of Life Sciences Zhejiang UniversityHangzhouZhejiang 310058China Plant Germplasm and Genomics Center Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingYunnan 650201 China state Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China Department of Biological Sciences University of Alabama411 Mary Harmon Bryant HallTuscaloosaAL 35487USA Biology Department University of Massachusetts Amherst611 North Pleasant Street221 Morrill 3AmherstMA 01003 USA

Poaceae(the grasses)includes rice,maize,wheat,and other crops,and is the most economically important angiosperm *** is also one of the largest plant families,consisting of over 11000 species with a global distribution that contributes to diverse *** species are classified into 12 subfamilies,with generally strong phylogenetic support for their ***,many relationships within subfamilies,among tribes and/or subtribes,remain *** better resolve the Poaceae phylogeny,we generated 342 transcriptomic and seven genomic datasets;these were combined with other genomic and transcriptomic datasets to provide sequences for 357 Poaceae species in 231 genera,representing 45 tribes and all 12 *** 1200 low-copy nuclear genes were retrieved from these datasets,with several subsets obtained using additional criteria,and used for coalescent analyses to reconstruct a Poaceae *** results strongly support the monophyly of 11 subfamilies;however,the subfamily Puelioideae was separated into two non-sister clades,one for each of the two previously defined tribes,supporting a hypothesis that places each tribe in a separate *** clock analyses estimated the crown age of Poaceae to be101 million years *** character reconstruction of C3/C4 photosynthesis supports the hypothesis of multiple independent origins of C4 *** origins are further supported by phylogenetic analysis of the ppc gene family that encodes the phosphoenolpyruvate carboxylase,which suggests that members of three paralogous subclades(ppc-aL1a,ppc-aL1b,and ppcB2)were recruited as functional C4 ppc *** study provides valuable resources and a robust phylogenetic framework for evolutionary analyses of the grass family.

关键词： Gramineae transcriptome nuclear phylogeny molecular clock C4 photosynthesis ppc gene evolution

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Survival is negatively associated with glucocorticoids in a wild ungulate neonate

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Integrative Zoology 2021年第2期16卷 214-225页

作者： Tess Michelle GINGERY Duane Richard DIEFENBACH Catharine ElizabethPRITCHARD David Charles ENSMINGER Bret Daniel WALLINGFORD Christopher Scott ROSENBERRY pennsylvania Cooperative Fish and Wildlife Research Unit Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA U.S.Geological Survey Pennsylvania Cooperative Fish and Wildlife Research UnitPennsylvania State UniversityUniversity ParkPennsylvaniaUSA Department of Ecosystem Science and Management Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA pennsylvania Game Commission 2001 Elmerton AvenueHarrisburgPennsylvaniaUSA Department of Integrative Biology University of CaliforniaBerkeleyValley Life Sciences BuildingBerkeleyCaliforniaUSA

It is unknown how ungulate physiological responses to environmental perturbation influence overall population ***,neonatal physiological responses remain poorly studied despite the importance of neonatal survival to population ***(GC)hormones potentially facilitate critical physiological and behavioral responses to environmental ***,elevated GC concentrations over time may compromise body condition and indirectly reduce *** evaluated baseline salivary cortisol(CORT;a primary GC in mammals)concentrations in 19 wild neonatal white-tailed deer(Odocoileus virginianus)in a northern(NS)and southern(SS)area in *** ranking survival models consisting of variables hypothesized to influence neonate survival(***,sex),the probability of neonate survival was best explained by CORT concentrations,where elevated CORT concentrations were associated with reduced survival probability to 12 weeks of *** concentrations were greater in the SS where predation rates and predator densities were *** the first evaluation of baseline CORT concentrations in an ungulate neonate to our knowledge,this is also the first study to demonstrate CORT concentrations are negatively associated with ungulate survival at any life *** hormones could provide a framework in which to better understand susceptibility to mortality in neonatal white-tailed deer.

关键词： neonates salivary cortisol stress survival ungulates

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