Academy of Sciences Republic of Uzbekistan

Porous carbons that are three-dimensionally periodic on the scale of optical wavelengths were made by a synthesis route resembling the geological formation of natural opal. Porous silica opal crystals were sintered to form an intersphere interface through which the silica was removed after infiltration with carbon or a carbon precursor. The resulting porous carbons had different structures depending on synthesis conditions. Both diamond and glassy carbon inverse opals resulted from volume filling. Graphite inverse opals, comprising 40-angstrom-thick layers of graphite sheets tiled on spherical surfaces, were produced by surface templating. The carbon inverse opals provide examples of both dielectric and metallic optical photonic crystals. They strongly diffract light and may provide a route toward photonic band-gap materials.

The mammalian target of rapamycin (mTOR) is a protein kinase that controls cellular metabolism, catabolism, immune responses, autophagy, survival, proliferation, and migration, to maintain cellular homeostasis. The mTOR signaling cascade consists of two distinct multi-subunit complexes named mTOR complex 1/2 (mTORC1/2). mTOR catalyzes the phosphorylation of several critical proteins like AKT, protein kinase C, insulin growth factor receptor (IGF-1R), 4E binding protein 1 (4E-BP1), ribosomal protein S6 kinase (S6K), transcription factor EB (TFEB), sterol-responsive element-binding proteins (SREBPs), Lipin-1, and Unc-51-like autophagy-activating kinases. mTOR signaling plays a central role in regulating translation, lipid synthesis, nucleotide synthesis, biogenesis of lysosomes, nutrient sensing, and growth factor signaling. The emerging pieces of evidence have revealed that the constitutive activation of the mTOR pathway due to mutations/amplification/deletion in either mTOR and its complexes (mTORC1 and mTORC2) or upstream targets is responsible for aging, neurological diseases, and human malignancies. Here, we provide the detailed structure of mTOR, its complexes, and the comprehensive role of upstream regulators, as well as downstream effectors of mTOR signaling cascades in the metabolism, biogenesis of biomolecules, immune responses, and autophagy. Additionally, we summarize the potential of long noncoding RNAs (lncRNAs) as an important modulator of mTOR signaling. Importantly, we have highlighted the potential of mTOR signaling in aging, neurological disorders, human cancers, cancer stem cells, and drug resistance. Here, we discuss the developments for the therapeutic targeting of mTOR signaling with improved anticancer efficacy for the benefit of cancer patients in clinics.

By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization's decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages.

It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

Despite rapidly decreasing costs and innovative technologies, sequencing of angiosperm genomes is not yet undertaken lightly. Generating larger amounts of sequence data more quickly does not address the difficulties of sequencing and assembling complex genomes de novo. The cotton (Gossypium spp.) genomes represent a challenging case. To this end, a coalition of cotton genome scientists has developed a strategy for sequencing the cotton genomes, which will vastly expand opportunities for cotton research and improvement worldwide. Cotton bolls at maturity (A) and cotton fibers under electron microscope (B). Photos courtesy of Mike Doughtery from the National Cotton Council (A) and Barbara Triplet (B). Cotton production provides income for approximately 100 million families, and approximately 150 countries are involved in cotton import and export. Its economic impact is estimated to be approximately $500 billion/year worldwide. China is the largest producer and consumer of raw cotton, but more than 80 countries, including Australia, some African countries, India, Pakistan, the United States, Mexico, and Uzbekistan, also produce cotton. The United States is the second largest producer, and grows cotton worth approximately $6 billion/year for fiber and approximately $1 billion/year for cottonseed oil and meal. Cotton is a major economic driver for some developing countries, like Uzbekistan, which annually produces approximately 4 million tons of raw cotton and exports fiber worth approximately $900 million. Cotton fiber is an outstanding model for the study of plant cell elongation and cell wall and cellulose biosynthesis (Kim and Triplett, 2001). Each seed has approximately 25,000 cotton fibers, each of which is a single and greatly elongated cell from the epidermal layer of the ovule (Fig. 1B). The fiber is composed of nearly pure cellulose, the largest component of plant biomass. Compared to lignin, cellulose is easily convertible to biofuels. Translational genomics of cotton fiber and cellulose may lead to the improvement of diverse biomass crops. The genus Gossypium includes approximately 45 diploid (2n = 2x = 26) and five tetraploid (2n = 4x = 52) species, all exhibiting disomic patterns of inheritance. Diploid species (2n = 26) fall into eight genomic groups (A–G, and K). The African clade, comprising the A, B, E, and F genomes (Wendel and Cronn, 2003), occurs naturally in Africa and Asia, while the D genome clade is indigenous to the Americas. A third diploid clade, including C, G, and K, is found in Australia. All 52 chromosome species, including Gossypium hirsutum and Gossypium barbadense, are classic natural allotetraploids that arose in the New World from interspecific hybridization between an A genome-like ancestral African species and a D genome-like American species. The closet extant relatives of the original tetraploid progenitors are the A genome species Gossypium herbaceum (A1) and Gossypium arboreum (A2) and the D genome species Gossypium raimondii (D5) ‘Ulbrich’ (Brubaker et al., 1999). Polyploidization is estimated to have occurred 1 to 2 million years ago (Wendel and Cronn, 2003), giving rise to five extant allotetraploid species. Interestingly, the A genome species produce spinnable fiber and are cultivated on a limited scale, whereas the D genome species do not (Applequist et al., 2001). More than 95% of the annual cotton crop worldwide is G. hirsutum, Upland or American cotton, and the extra-long staple or Pima cotton (G. barbadense) accounts for less than 2% (National Cotton Council, http://www.cotton.org, 2006). Understanding the contribution of the A and D subgenomes to gene expression in the allotetraploids may facilitate improving fiber traits (Jiang et al., 1998; Saha et al., 2006; Yang et al., 2006). Decoding cotton genomes will be a foundation for improving understanding of the functional and agronomic significance of polyploidy and genome size variation within the Gossypium genus. The haploid genome sizes are estimated to be approximately 880 Mb for G. raimondii ‘Ulbrich’, approximately 1.75 Gb for G. arboreum, and approximately 2.5 Gb for G. hirsutum (Hendrix and Stewart, 2005). Variation in DNA content in the diploid species reflects increases and decreases in copy numbers of various repeat families (Zhao et al., 1998), especially retrotransposon-like elements (Hawkins et al., 2006). DNA content of the allopolyploids is approximately the sum of the A and D genome progenitors, and nearly all of the approximately 22,000 amplified fragment length polymorphism fragments surveyed are additive in the allopolyploids (Liu et al., 2001). This suggests a role of genetic and epigenetic mechanisms for gene expression in phenotypic variation and selection of allotetraploid species (Jiang et al., 1998; Wendel, 2000; Adams et al., 2003; Yang et al., 2006; Chen, 2007). Genomic resources such as bacterial artificial chromosomes (BACs), ESTs, linkage maps, and integrated genetic and physical maps provide landmarks for sequence analysis and assembly. Linkage maps in tetraploid cotton have been most densely populated by analysis of interspecific G. hirsutum × G. barbadense F2 families (Reinisch et al., 1994; Rong et al., 2004) and backcross lines (Lacape et al., 2005; Guo et al., 2007) due to low levels of DNA polymorphism within cotton species. Mapping populations have also been developed for G. hirsutum × Gossypium tomentosum F2 (Waghmare et al., 2005) and Gossypium mustelinum × G. hirsutum (P. Chee and A. Paterson, unpublished data). Molecular marker linkage groups were localized and orientated with various interspecific hypoaneuploid F1 hybrids available for most chromosomes, and elsewhere by in situ hybridization (Hanson et al., 1995; Saha et al., 2006; Wang et al., 2006;,Ji et al., 2007). Synteny and locus order were also determined by wide-cross whole-genome radiation hybrid mapping, a method complementary to other forms of cotton genome mapping (Gao et al., 2006). At least a dozen genetic maps of crosses between diverse cotton species and genotypes are available, most made to map specific traits and quantitative trait loci (QTLs). Some of these maps collectively include approximately 5,000 DNA markers (approximately 3,300 restriction fragment length polymorphisms, approximately 700 amplified fragment length polymorphisms, approximately 1,000 simple sequence repeats, and approximately 100 single nucleotide polymorphisms). In addition, sequence-tagged site-based maps consisting of 2,584 loci at 1.72-cM (approximately 600 kb) intervals in tetraploids (AD genomes), 1,014 loci at 1.42-cM (approximately 600 kb) intervals in diploids (D genome; Rong et al., 2004, 2005), and an EST-simple sequence repeat-based genetic map of 1,710 loci at 1.92-cM intervals in tetraploids (AD genomes; Guo et al., 2007) are available. There is a high degree of colinearity among the respective genome types (Rong et al., 2005). Of particular long-term value are permanent recombinant inbred lines (RILs) and chromosome substitution lines. RILs have already begun to contribute to QTL definition, e.g. for a G. hirsutum × G. barbadense cross (Frelichowski et al., 2006) and intraspecific crosses within G. hirsutum (Ulloa et al., 2005; Abdurakhmonov et al., 2007; Shen et al., 2007). Near-isogenic disomic substitution lines of G. hirsutum enable the localization of net phenotypic effects. Moreover, chromosome-specific RILs enable high-resolution QTL definition and mapping (Stelly et al., 2005). Reference maps have incorporated diverse types and sources of DNA markers. Jean-Marc Lacape and his colleagues have integrated linkage maps developed by researchers in China (T. Zhang), France (J.M. Lacape), and the United States (A. Paterson and M. Ulloa) into TropGENE-DB (http://tropgenedb.cirad.fr/en/cotton.html) using a CMap comparative map viewer (Nguyen et al., 2004). A similar map viewer has been implemented in the CottonDB (http://cottondb.org) and the Cotton Microsatellite Database (http://www.cottonmarker.org) that contains approximately 8,000 microsatellites (Blenda et al., 2006). The further development of comprehensive linkage maps will be used to anchor and assemble genomic sequences. BAC libraries have been developed for several G. hirsutum cultivars (‘0–613-2R’, ‘Acala Maxxa’, ‘Auburn 623’, ‘Tamcot HQ95’, and ‘TM-1’), G. barbadense (‘Pima S6’), two G. arboreum strains (AKA8401 and Jinglinzhongmian), G. raimondii, Gossypium longicalyx, and an outgroup (Gossypioides kirkii). A total of 10 genome equivalents of G. raimondii BACs has been fingerprinted using standard procedures (Marra et al., 1997). All genetically mapped probes have been incorporated into the fingerprint assembly using the overlapping oligonucleotides hybridization method (Cai et al., 1998). The assembly will be publicly available via a WebFPC site and incorporated into the existing BACMan resource at the Plant Genome Mapping Laboratory (www.plantgenome.uga.edu). A G. hirsutum L. ‘TM-1’ library has been used to develop integrated genetic and physical maps (R. Kohel, J. Yu, and T. Zhang, unpublished data). A G. hirsutum L. ‘0-613-2R’ library has been successfully used to locate the restorer of fertility gene in a 100-kb region (Yin et al., 2006) and to assign linkage groups to identified chromosomes using BAC-fluorescence in situ hybridization (FISH; Wang et al., 2006). As of July 18, 2007, 356,889 Gossypium sequences were in GenBank, including 40,069 ESTs from G. arboreum (A), 67,098 from G. raimondii (D), 232,006 from G. hirsutum (AD tetraploid), and a few from other Gossypium members (Arpat et al., 2004; Udall et al., 2006; Yang et al., 2006; Taliercio and Boykin, 2007). Among these ESTs, many are from developing fiber and are enriched in putative MYB and WRKY transcription factors and phytohormone regulators (Yang et al., 2006). Transcription factors in these families are known to be important in the development of Arabidopsis (Arabidopsis thaliana) leaf trichomes, and phytohormonal effects on fiber cell development in immature cotton ovules cultured in vitro are well documented (Beasley and Ting, 1974). Moreover, A subgenome ESTs of all functional classifications are dramatically enriched in G. hirsutum fiber (Yang et al., 2006), a result consistent with the production of long lint fibers in A genome species. Some ESTs have been used to develop sequence-specific markers in breeding and to construct microarrays, leading to the identification of many candidate genes involved in fiber cell initiation and elongation (Arpat et al., 2004; Lee et al., 2006; Shi et al., 2006; Wu et al., 2006; Udall et al., 2007). The Malvales (including cotton) are the nearest relative to Arabidopsis outside of the Brassicales for which detailed genetic and physical maps have been described (Bowers et al., 2003). Comparative analyses reveal a considerable degree of synteny/colinearity between the ancestral cotton and Arabidopsis genomes. A total of 1,738 (62%) sequenced loci in cotton had matches in Arabidopsis (Rong et al., 2005). Gaining access to the unique features that distinguish cotton from other plants both as an economic crop and a botanical model might benefit from translational genomics, leveraging of structural and functional information from Arabidopsis. A comprehensive strategy needs to consider present needs along with long-term goals in relation to economics, technology, and priorities. A strong case can be made for complete sequencing of one or more representatives of each Gossypium genome group, A, B, C, D, E, F, G, K, and a tetraploid-derived AD (n = 26) genome (Paterson, 2006). Continuing progress in sequencing throughput and cost reduction will render this goal increasingly feasible and desirable. Sequencing representatives from each diploid clade will be important for molecular dissection of evolutionary patterns and biological phenomena, including the genomic and morphological diversity that has permitted species within the genus to adapt to a wide range of ecosystems in warmer and arid regions of the world. Sequences from A and D genome diploid species will aid tetraploid AD genome sequence assembly and could prove to be invaluable for revealing differences in gene content and expression patterns across the ploidy levels and for providing insight into polyploid genome evolution. Although there is an approximately 3-fold variation in genome size among the diploids, the high degree of conservation of gene order at the macro level between diploids and tetraploids (Brubaker et al., 1999; Rong et al., 2004; Desai et al., 2006) suggests that the vast majority of sequence data from diploids will extrapolate directly to tetraploids. Sequencing an elite G. hirsutum genome, AD, will provide the ultimate reference and resource for application-oriented structural, functional, and bioinformatic needs for the species that accounts for >95% of world cotton production. Sequencing an elite G. arboreum or G. herbaceum genome will provide valuable data on fiber genes. Comparisons of four species across two ploidy levels, including A1, A2, D5, and AD tetraploid subgenomes, will provide clues as to how polyploidy and domestication “interact.” Parallel comparisons between domesticated and nondomesticated forms of the A and AD genome species will shed light on the effects of artificial versus natural selection. Based on these considerations, one can envision multiple and parallel approaches to reveal genome diversity and complete genome information of Gossypium genomes. Additional ESTs should be sequenced from other diploid (e.g. C, G, and K genomes) and tetraploid (e.g. G. barbadense, AD) clades and in late fiber development stages such as secondary wall biosynthesis (Haigler et al., 2005). Sequencing using gene enrichment techniques such as methylation filtration and Cot-based cloning that appear to offer complementary coverage of the low-copy DNA will generate novel genomic sequences that are absent in EST collections. A pilot study in methylation filtration comparing G. raimondii, G. arboreum, G. hirsutum, and G. barbadense is under way (B.E. Scheffler, S. Saha, and Orion Genomics, unpublished data). The whole-genome shotgun sequence of the smallest Gossypium genome, G. raimondii (approximately 880 Mb), will provide fundamental information about gene content and organization. The U.S. Department of Energy Joint Genome Institutes (http://www.jgi.doe.gov/) has selected G. raimondii for a pilot study for shotgun sequencing at 0.5× coverage to better define the genome and establish a workable strategy for its complete sequencing. A partially or fully sequenced G. raimondii genome will establish the critical initial template for characterizing the spectrum of diversity among the eight Gossypium genome types and three polyploid clades (Wendel and Cronn, 2003). A survey of approximately 100 of the most abundant repetitive families in the tetraploid genome showed only four to be abundant in the D genome but rare or absent in the A genome (Zhao et al., 1998), which diverged from the D genome of G. raimondii about 5 to 10 million years ago (Senchina et al., 2003). Thus, most high-copy repetitive DNA families in the D genome are at least 5 to 10 million years old and likely to be amenable to assembly by a whole-genome shotgun approach. A BAC-based AD genome sequence may offer superior opportunities to elucidate the types and frequencies of changes that distinguish polyploid from diploid cottons. The process could be greatly enhanced by using the finished genome sequence of a diploid species as a template and guide. Intergenomic concerted evolution and the presence of recently amplified repetitive DNA families would be problematic for a whole-genome shotgun approach. A reasonable approach is to establish minimum tiling path of fingerprinted contigs of G. hirsutum homoeologous chromosomes. This goal can be achieved by developing integrated homoeologous chromosome maps that include anchored DNA markers in linkage maps and BAC-end sequences in physical maps that can be further validated by radiation hybrid mapping and/or BAC-FISH (Hanson et al., 1995; Wang et al., 2006). FISH of landed BACs indicated that homoeologous segments were readily detectable by BAC-FISH for low-copy probes and that they seemed amenable to differentiation on the basis of FISH signal strength (Wang et al., 2007). Large duplicated segments have been reported within individual corresponding homoeologous chromosomes, suggesting ancient or recent genome expansion in cotton genomes (Rong et al., 2005; Wang et al., 2007). It will be prudent to sequence and assemble representative homoeologous BACs and/or a few pairs of homoeologous chromosomes prior to large-scale sequencing of G. hirsutum tetraploid genomes. The cotton community and industry are cooperatively developing workshops and communication methods for planning, coordinating, and executing sequencing and post-sequencing activities. The key questions under consideration are: (1) which species should we sequence; and (2) which techniques should be used for each genome? In the long term, a singularly important goal will be to establish the complete genome sequence of the most widely cultivated cotton, i.e. G. hirsutum. Given its genomic redundancies, size (approximately 2.5 polyploid and other we a to approaches that range from to on sequence from genomes, e.g. G. raimondii and G. herbaceum or G. this long-term we envision the specific shotgun sequencing of G. raimondii, a of cultivated and among the smallest Gossypium genomes, to provide fundamental information about gene content and organization. Comparative sequencing of corresponding segments of tetraploid G. hirsutum to reveal the likely to be complete sequencing. and a strategy to sequence of G. hirsutum. This may well of a minimum tiling path of contigs of G. hirsutum homoeologous chromosomes. bioinformatic and to and the information to the cotton and of sequence information should functional and structural genomic resources at the molecular and in levels, sequence for genome and expression detailed of the cotton genome sequence to gene and cloning in this species, a large-scale for DNA sequence diversity nucleotide and facilitate high-resolution whole-genome develop genomic tiling to gene expression and analysis of biological and agronomic and sequence and and and To and of comprehensive cotton genomic the most important factors to consider are data and and data analysis and To genomic research in cotton, the Cotton Genome in with a to of the and of the cotton genome for the benefit of the A site will be identified to establish a that will researchers to and about cotton genome sequencing and genomic The of data from various sequencing will be and to for many is to develop a data that can facilitate access and of genomic and sequence In to the CMap and Cotton Microsatellite CottonDB (http://cottondb.org) provides and including genetic and physical maps, trait and The Cotton the community a single of to Cotton the Cotton Database et al., 2006), provides for an to and comparative and is integrated with comparative and genomic sequence expression and the for Cotton consisting of approximately from ESTs can be found at the site There is a to expand bioinformatic for and the cotton genomic sequences that will be in the A model community is The Arabidopsis The cotton sequence of the should be to and cotton information resources in cotton using genome and gene Some existing may be to a of data and community but resources will be to key bioinformatic A for sequencing polyploid genomes is the among and homoeologous sequences in diploid and allotetraploid species. Gossypium species are (Bowers et al., 2003; Rong et al., 2005). Moreover, allopolyploids two or more of homoeologous chromosomes, leading to genetic and epigenetic changes in subgenomes and 2007). bioinformatic and for assembly and of genomes is a for sequencing cotton and other polyploid genomes such as and A sequenced cotton genome will provide a reference for many genomes in Gossypium species using and sequencing (e.g. and 2006). The of will be to establish a reference sequence anchored to physical and genetic This sequence will be used to and genomes and to the gene and basis of phenotypic and evolutionary diversity for cotton cotton genomes will fundamental research on genome and gene cell differentiation and cellulose cell molecular of cell wall and will include improvement of biological key to and production of and and biomass as well as of cotton and will be by improvement in elements key to all of e.g. improvement of and and reduction of and some are more than the and are on both and The community is and of the and value of sequencing cotton genomes. for a cotton genome sequencing and for and from the members of the Cotton Genome members of the cotton genomics and breeding community for and for not many to for cotton research is by from the National U.S. Department of Cotton National of and groups and in Australia, India, Pakistan, the United States, Uzbekistan, and The Cotton Genome Sequencing can be found at

The nonrecombining portion of the human Y chromosome has proven to be a valuable tool for the study of population history. The maintenance of extended haplotypes characteristic of particular geographic regions, despite extensive admixture, allows complex demographic events to be deconstructed. In this study we report the frequencies of 23 Y-chromosome biallelic polymorphism haplotypes in 1,935 men from 49 Eurasian populations, with a particular focus on Central Asia. These haplotypes reveal traces of historical migrations, and provide an insight into the earliest patterns of settlement of anatomically modern humans on the Eurasian continent. Central Asia is revealed to be an important reservoir of genetic diversity, and the source of at least three major waves of migration leading into Europe, the Americas, and India. The genetic results are interpreted in the context of Eurasian linguistic patterns.

In July 2012, the ATLAS and CMS collaborations at the CERN Large Hadron Collider announced the observation of a Higgs boson at a mass of around 125 gigaelectronvolts. Ten years later, and with the data corresponding to the production of a 30-times larger number of Higgs bosons, we have learnt much more about the properties of the Higgs boson. The CMS experiment has observed the Higgs boson in numerous fermionic and bosonic decay channels, established its spin-parity quantum numbers, determined its mass and measured its production cross-sections in various modes. Here the CMS Collaboration reports the most up-to-date combination of results on the properties of the Higgs boson, including the most stringent limit on the cross-section for the production of a pair of Higgs bosons, on the basis of data from proton-proton collisions at a centre-of-mass energy of 13 teraelectronvolts. Within the uncertainties, all these observations are compatible with the predictions of the standard model of elementary particle physics. Much evidence points to the fact that the standard model is a low-energy approximation of a more comprehensive theory. Several of the standard model issues originate in the sector of Higgs boson physics. An order of magnitude larger number of Higgs bosons, expected to be examined over the next 15 years, will help deepen our understanding of this crucial sector.

Compared to the conventional linkage mapping, linkage disequilibrium (LD)-mapping, using the nonrandom associations of loci in haplotypes, is a powerful high-resolution mapping tool for complex quantitative traits. The recent advances in the development of unbiased association mapping approaches for plant population with their successful applications in dissecting a number of simple to complex traits in many crop species demonstrate a flourish of the approach as a "powerful gene tagging" tool for crops in the plant genomics era of 21st century. The goal of this review is to provide nonexpert readers of crop breeding community with (1) the basic concept, merits, and simple description of existing methodologies for an association mapping with the recent improvements for plant populations, and (2) the details of some of pioneer and recent studies on association mapping in various crop species to demonstrate the feasibility, success, problems, and future perspectives of the efforts in plants. This should be helpful for interested readers of international plant research community as a guideline for the basic understanding, choosing the appropriate methods, and its application.

Ion-specific standards are needed to protect biodiversity

Global food demand is expected to nearly double by 2050 due to an increase in the world's population. The Green Revolution has played a key role in the past century by increasing agricultural productivity worldwide, however, limited availability and continued depletion of natural resources such as arable land and water will continue to pose a serious challenge for global food security in the coming decades. High yielding varieties with proven tolerance to biotic and abiotic stresses, superior nutritional profiles, and the ability to adapt to the changing environment are needed for continued agricultural sustainability. The narrow genetic base of modern cultivars is becoming a major bottleneck for crop improvement efforts and, therefore, the use of crop wild relatives (CWRs) is a promising approach to enhance genetic diversity of cultivated crops. This article provides a review of the efforts to date on the exploration of CWRs as a source of tolerance to multiple biotic and abiotic stresses in four global crops of importance; maize, rice, cotton, and soybean. In addition to the overview of the repertoire and geographical spread of CWRs in each of the respective crops, we have provided a comprehensive discussion on the morphological and/or genetic basis of the traits along with some examples, when available, of the research in the transfer of traits from CWRs to cultivated varieties. The emergence of modern molecular and genomic technologies has not only accelerated the pace of dissecting the genetics underlying the traits found in CWRs, but also enabled rapid and efficient trait transfer and genome manipulation. The potential and promise of these technologies has also been highlighted in this review.

The dynamics of localized excitations in an array of Bose-Einstein condensates (BECs) is investigated in the framework of the nonlinear lattice theory. The existence of temporarily stable ground states displaying an atomic population distribution localized on very few lattice sites (intrinsic localized modes), as well as atomic population distributions involving many lattice sites (envelope solitons), is studied both numerically and analytically. The origin and properties of these modes are shown to be inherently connected with the interplay between macroscopic quantum tunneling and nonlinearity-induced self-trapping of atoms in coupled BECs. The phenomenon of Bloch oscillations of these excitations is studied both for zero and nonzero backgrounds. We find that in a definite range of parameters, homogeneous distributions can become modulationally unstable. We also show that bright solitons and excitations of shock-wave type can exist in BEC arrays even in the case of positive scattering length. Finally, we argue that a BEC array with negative scattering length in the presence of linear potentials can display collapse.

Societal Impact Statement Research and publication of the planet's remaining plant and fungal species as yet unknown to science is essential if we are to address the United Nations Sustainable Development Goal (SDG) 15 “Life on Land” which includes the protection of terrestrial ecosystems and halting of biodiversity loss. If species are not known to science, they cannot be assessed on the International Union for Conservation of Nature (IUCN) Red List of Threatened Species and so the possibility to protect them from extinction is reduced. Furthermore, until species are known to science they cannot be fully scientifically evaluated for their potential as new foods, medicines, and products which would help address SDGs 1,2,3, and 8. Summary Scientific discovery, including naming new taxa, is important because without a scientific name, a species is invisible to science and the possibilities of researching its ecology, applications and threats, and conserving it, are greatly reduced. We review new scientific discoveries in the plant and fungal kingdoms, based largely on new names of taxa published in 2019 and indexed in the International Plant Names Index and Index Fungorum. Numbers of new species in both kingdoms were similar with 1942 new species of plant published and 1882 species of fungi. However, while >50% of plant species have likely been discovered, >90% of fungi remain unknown. This gulf likely explains the greater number of higher order taxa for fungi published in 2019: three classes, 18 orders, 48 families and 214 genera versus one new family and 87 new genera for plants. We compare the kingdoms in terms of rates of scientific discovery, globally and in different taxonomic groups and geographic areas, and with regard to the use of DNA in discovery. We review species new to science, especially those of interest to humanity as new products, and also by life‐form. We consider where future such discoveries can be expected. We recommend an urgent increase in investment in scientific discovery of plant and fungal species, while they still survive. Priorities include more investment in training taxonomists, in building and equipping collections‐based research centers for them, especially in species‐rich, income‐poor countries where the bulk of species as yet unknown to science are thought to occur.

This article is the 13th contribution in the Fungal Diversity Notes series, wherein 125 taxa from four phyla, ten classes, 31 orders, 69 families, 92 genera and three genera incertae sedis are treated, demonstrating worldwide and geographic distribution. Fungal taxa described and illustrated in the present study include three new genera, 69 new species, one new combination, one reference specimen and 51 new records on new hosts and new geographical distributions. Three new genera, Cylindrotorula (Torulaceae), Scolecoleotia (Leotiales genus incertae sedis) and Xenovaginatispora (Lindomycetaceae) are introduced based on distinct phylogenetic lineages and unique morphologies. Newly described species are Aspergillus lannaensis, Cercophora dulciaquae, Cladophialophora aquatica, Coprinellus punjabensis, Cortinarius alutarius, C. mammillatus, C. quercoflocculosus, Coryneum fagi, Cruentomycena uttarakhandina, Cryptocoryneum rosae, Cyathus uniperidiolus, Cylindrotorula indica, Diaporthe chamaeropicola, Didymella azollae, Diplodia alanphillipsii, Dothiora coronicola, Efibula rodriguezarmasiae, Erysiphe salicicola, Fusarium queenslandicum, Geastrum gorgonicum, G. hansagiense, Helicosporium sexualis, Helminthosporium chiangraiensis, Hongkongmyces kokensis, Hydrophilomyces hydraenae, Hygrocybe boertmannii, Hyphoderma australosetigerum, Hyphodontia yunnanensis, Khaleijomyces umikazeana, Laboulbenia divisa, Laboulbenia triarthronis, Laccaria populina, Lactarius pallidozonarius, Lepidosphaeria strobelii, Longipedicellata megafusiformis, Lophiotrema lincangensis, Marasmius benghalensis, M. jinfoshanensis, M. subtropicus, Mariannaea camelliae, Melanographium smilaxii, Microbotryum polycnemoides, Mimeomyces digitatus, Minutisphaera thailandensis, Mortierella solitaria, Mucor harpali, Nigrograna jinghongensis, Odontia huanrenensis, O. parvispina, Paraconiothyrium ajrekarii, Parafuscosporella niloticus, Phaeocytostroma yomensis, Phaeoisaria synnematicus, Phanerochaete hainanensis, Pleopunctum thailandicum, Pleurotheciella dimorphospora, Pseudochaetosphaeronema chiangraiense, Pseudodactylaria albicolonia, Rhexoacrodictys nigrospora, Russula paravioleipes, Scolecoleotia eriocamporesi, Seriascoma honghense, Synandromyces makranczyi, Thyridaria aureobrunnea, Torula lancangjiangensis, Tubeufia longihelicospora, Wicklowia fusiformispora, Xenovaginatispora phichaiensis and Xylaria apiospora. One new combination, Pseudobactrodesmium stilboideus is proposed. A reference specimen of Comoclathris permunda is designated. New host or distribution records are provided for Acrocalymma fici, Aliquandostipite khaoyaiensis, Camarosporidiella laburni, Canalisporium caribense, Chaetoscutula juniperi, Chlorophyllum demangei, C. globosum, C. hortense, Cladophialophora abundans, Dendryphion hydei, Diaporthe foeniculina, D. pseudophoenicicola, D. pyracanthae, Dictyosporium pandanicola, Dyfrolomyces distoseptatus, Ernakulamia tanakae, Eutypa flavovirens, E. lata, Favolus septatus, Fusarium atrovinosum, F. clavum, Helicosporium luteosporum, Hermatomyces nabanheensis, Hermatomyces sphaericoides, Longipedicellata aquatica, Lophiostoma caudata, L. clematidis-vitalbae, Lophiotrema hydei, L. neoarundinaria, Marasmiellus palmivorus, Megacapitula villosa, Micropsalliota globocystis, M. gracilis, Montagnula thailandica, Neohelicosporium irregulare, N. parisporum, Paradictyoarthrinium diffractum, Phaeoisaria aquatica, Poaceascoma taiwanense, Saproamanita manicata, Spegazzinia camelliae, Submersispora variabilis, Thyronectria caudata, T. mackenziei, Tubeufia chiangmaiensis, T. roseohelicospora, Vaginatispora nypae, Wicklowia submersa, Xanthagaricus necopinatus and Xylaria haemorrhoidalis. The data presented herein are based on morphological examination of fresh specimens, coupled with analysis of phylogenetic sequence data to better integrate taxa into appropriate taxonomic ranks and infer their evolutionary relationships.

This paper is the seventh in the Fungal Diversity Notes series, where 131 taxa accommodated in 28 families are mainly described from Rosa ( Rosaceae ) and a few other hosts. Novel fungal taxa are described in the present study, including 17 new genera, 93 new species, four combinations, a sexual record for a species and new host records for 16 species. Bhatiellae , Cycasicola , Dactylidina , Embarria , Hawksworthiana , Italica , Melanocucurbitaria , Melanodiplodia , Monoseptella , Uzbekistanica , Neoconiothyrium , Neopaucispora , Pararoussoella , Paraxylaria , Marjia , Sporormurispora and Xenomassariosphaeria are introduced as new ascomycete genera. We also introduce the new species Absidia jindoensis , Alternaria doliconidium , A . hampshirensis , Angustimassarina rosarum , Astragalicola vasilyevae , Backusella locustae , Bartalinia rosicola , Bhatiellae rosae , Broomella rosae , Castanediella camelliae , Coelodictyosporium rosarum , Comoclathris rosae , C . rosarum , Comoclathris rosigena , Coniochaeta baysunika , C. rosae , Cycasicola goaensis , Dactylidina shoemakeri , Dematiopleospora donetzica , D . rosicola , D . salsolae , Diaporthe rosae , D . rosicola , Endoconidioma rosae - hissaricae , Epicoccum rosae , Hawksworthiana clematidicola , H . lonicerae , Italica achilleae , Keissleriella phragmiticola , K . rosacearum , K . rosae , K . rosarum , Lophiostoma rosae , Marjia tianschanica , M . uzbekistanica , Melanocucurbitaria uzbekistanica , Melanodiplodia tianschanica , Monoseptella rosae , Mucor fluvius , Muriformistrickeria rosae , Murilentithecium rosae , Neoascochyta rosicola , Neoconiothyrium rosae , Neopaucispora rosaecae , Neosetophoma rosarum , N . rosae , N . rosigena , Neostagonospora artemisiae , Ophiobolus artemisiicola , Paraconiothyrium rosae , Paraphaeosphaeria rosae , P . rosicola , Pararoussoella rosarum , Parathyridaria rosae , Paraxylaria rosacearum , Penicillium acidum , P . aquaticum , Phragmocamarosporium rosae , Pleospora rosae , P . rosae - caninae , Poaceicola agrostina , P . arundinicola , P . rosae , Populocrescentia ammophilae , P . rosae , Pseudocamarosporium pteleae , P . ulmi - minoris , Pseudocercospora rosae , Pseudopithomyces rosae , Pseudostrickeria rosae , Sclerostagonospora lathyri , S . rosae , S . rosicola , Seimatosporium rosigenum , S . rosicola , Seiridium rosarum , Setoseptoria arundelensis , S . englandensis , S . lulworthcovensis , Sigarispora agrostidis , S . caryophyllacearum , S . junci , S . medicaginicola , S . rosicola , S . scrophulariae , S . thymi , Sporormurispora atraphaxidis , S . pruni , Suttonomyces rosae , Umbelopsis sinsidoensis , Uzbekistanica rosae - hissaricae , U . yakutkhanika , Wojnowicia rosicola , Xenomassariosphaeria rosae . New host records are provided for Amandinea punctata , Angustimassarina quercicola , Diaporthe rhusicola , D. eres , D. foeniculina , D. rudis , Diplodia seriata , Dothiorella iberica , Lasiodiplodia theobromae , Lecidella elaeochroma , Muriformistrickeria rubi , Neofusicoccum australe , Paraphaeosphaeria michotii , Pleurophoma pleurospora , Sigarispora caulium and Teichospora rubriostiolata . The new combinations are Dactylidina dactylidis (= Allophaeosphaeria dactylidis ), Embarria clematidis (= Allophaeosphaeria clematidis ), Hawksworthiana alliariae (= Dematiopleospora alliariae ) and Italica luzulae (= Dematiopleospora luzulae ). This study also provides some insights into the diversity of fungi on Rosa species and especially those on Rosa spines that resulted in the characterisation of eight new genera, 45 new species, and nine new host records. We also collected taxa from Rosa stems and there was 31% (20/65) overlap with taxa found on stems with that on spines. Because of the limited and non-targeted sampling for comparison with collections from spines and stems of the same host and location, it is not possible to say that the fungi on spines of Rosa differ from those on stems. The study however, does illustrate how spines are interesting substrates with high fungal biodiversity. This may be because of their hard structure resulting in slow decay and hence are suitable substrates leading to fungal colonisation. All data presented herein are based on morphological examination of specimens, coupled with phylogenetic sequence data to better integrate taxa into appropriate taxonomic ranks and infer their evolutionary relationships.

UBVR photometric monitoring of Herbig Ae/Be stars and some related objects has been carried out at Maidanak Observatory in Uzbekistan since 1983. More than 71,000 observations of about 230 stars have been obtained and are made available for anonymous ftp. Virtually all Herbig Ae/Be stars observed are irregular variables (called "UXors" after UX Ori), but there is a wide range of amplitudes from barely detectable to more than 4 mag in V . Our data confirm the results of previous studies, which indicate that large-amplitude variability is confined to stars with spectral types later than B8. The distribution of variability ranges is quite similar to what is seen in classical T Tauri stars. A careful search has failed to reveal any evidence for periodic variations up to 30 days, which can be interpreted as rotation periods. This is a clear distinction between the light variations of low-mass and high-mass pre–main-sequence stars. The Herbig Ae/Be stars evidently do not possess either the large, stable cool spots or persistent hot spots associated with strong surface magnetic fields and magnetically funneled accretion in classical T Tauri stars. A wide variety of shapes, timescales, and amplitudes exists, but the most common behavior is well illustrated by the light curve of LkHα 234. There are two principal components: (1) irregular variations on timescales of days around a mean brightness level that changes on a much longer timescale (typically years), sometimes in a quasi-cyclic fashion, and (2) occasional episodes of deep minima, occurring at irregular intervals but more frequently near the low points of the brightness cycles. Our data suggest that many T Tauri stars of K0 and earlier spectral type share the same variability characteristics as Herbig Ae/Be stars and should be regarded as UXors. Two FU Orionis stars ("FUors"), FU Ori and V1515 Cyg, also have recent light curves that are similar, in some respects, to UXors. The most developed model to account for the variations of some large-amplitude UXors involves variable obscuration by circumstellar dust clumps orbiting the star in a disk viewed nearly edge-on. However, there are problems in extending this model to the entire class, which lead us to propose an alternative mechanism, i.e., unsteady accretion. Evidence favoring the accretion model over the obscuration model is presented. It is suggested that the thermal instability mechanism responsible for outbursts in interacting binary system disks, and possibly FUors, may be the cause of the deep minima in UXors.

Most aqueous biological and technological systems contain solvated ions. Atomistic explicit-water simulations of ionic solutions rely crucially on accurate ionic force fields, which contain most commonly two adjustable parameters: the Lennard-Jones diameter and the interaction strength. Assuming these parameters to be properly optimized, the plethora of parameters one finds in the literature for one and the same ion is surprising. In principle, the two parameters should be uniquely determined by matching two ionic properties obtained for a particular water model and within a given simulation protocol with the corresponding experimental observables. Traditionally, ion parameters were chosen in a somewhat unsystematic way to reproduce the solvation free energy and to give the correct ion size when compared with scattering results. Which experimental observable one chooses to reproduce should in principle depend on the context within which the ionic force field is going to be used. In the present work we suggest to use the solvation free energy in conjunction with the solvation entropy to construct thermodynamically sound force fields for the alkali and halide ions for the simulation of ion-specific effects in aqueous environment. To that end we determine the solvation free energy and entropy of both cations and anions in the entire relevant parameter space. As an independent check on the quality of the resulting force fields we also determine the effective ionic radius from the first peak of the radial ion-water distribution function. Several difficulties during parameter optimization are discussed in detail. (i) Single-ion solvation depends decisively on water-air surface properties, which experimentally becomes relevant when introducing extrathermodynamic assumptions on the hydronium (H(3)O(+)) solvation energy. Fitting ion pairs circumvents this problem but leaves the parameters of one reference ion (here we choose chloride) undetermined. (ii) For the halides the problem is almost underdetermined, i.e., there is a whole set of degenerate parameters that equally well describe, e.g., chloride and bromide ions. (iii) For the heavy cations the problem is overdetermined, i.e., no combination of Lennard-Jones parameters is able to reproduce simultaneously energy and entropy of solvation. We discuss various possibilities to deal with these problems and finally present an optimized force field for the halide anions that reproduces the free energy and the entropy of solvation. For the alkali metal cations there is no unambiguous choice of parameters. Therefore, we give three different parameter sets for every ion with a small, intermediate, or large Lennard-Jones interaction strength, where the Lennard-Jones diameters are optimized to reproduce the solvation free energy. The ionic radius is reproduced with acceptable accuracy by this optimization strategy, meaning that the proposed force fields are reliable beyond the target observables (i.e., free energy and entropy of solvation).

from the Indus Valley. This process was likely stimulated at the onset of the current geological age, ~4.2 thousand years ago, by a widespread multicentury drought. In contrast to genome-wide admixture, mitochondrial DNA stasis supports that this introgression was male-driven, suggesting that selection of arid-adapted zebu bulls enhanced herd survival. This human-mediated migration of zebu-derived genetics has continued through millennia, altering tropical herding on each continent.

We propose a method to accelerate adiabatic dynamics of wave functions (WFs) in quantum mechanics to obtain a final adiabatic state except for the spatially uniform phase in any desired short time. In our previous work, acceleration of the dynamics of WFs was shown to obtain the final state in any short time by applying driving potential. We develop the previous theory of fast-forward to derive a driving potential for the fast-forward of adiabatic dynamics. A typical example is the fast-forward of adiabatic transport of a WF, which is the ideal transport in the sense that a stationary WF is transported to an aimed position in any desired short time without leaving any disturbance at the final time of the fast-forward. As other important examples, we show accelerated manipulations of WFs, such as their splitting and squeezing. The theory is also applicable to macroscopic quantum mechanics described by the nonlinear Schrödinger equation.

We point out a simple relation between the nuclear vertex constant (NVC) and the overall normalization of the astrophysical $S$ factor. Using predicted values of the NVC for the virtual decay of $^{8}\mathrm{B}\ensuremath{\rightarrow}^{7}\mathrm{Be}+p$ we find ${S}_{17}(0)\ensuremath{\approx}17.6$ eVb for $^{7}\mathrm{Be}{(p,\ensuremath{\gamma})}^{8}\mathrm{B}$ reactions, consistent with the low values extrapolated from direct capture measurements by Filippone et al. and by Vaughn et al. New possibilities, using proton transfer reactions, to measure the astrophysical $S$ factor indirectly are proposed.

The recent realistic estimate of fungal numbers which used various algorithms was between 2.2 and 3.8 million. There are nearly 100,000 accepted species of Fungi and fungus-like taxa, which is between 2.6 and 4.5% of the estimated species. Several forums such as Botanica Marina series, Fungal Diversity notes, Fungal Biodiversity Profiles, Fungal Systematics and Evolution—New and Interesting Fungi, Mycosphere notes and Fungal Planet have enhanced the introduction of new taxa and nearly 2000 species have been introduced in these publications in the last decade. The need to define a fungal species more accurately has been recognized, but there is much research needed before this can be better clarified. We address the evidence that is needed to estimate the numbers of fungi and address the various advances that have been made towards its understanding. Some genera are barely known, whereas some plant pathogens comprise numerous species complexes and numbers are steadily increasing. In this paper, we examine ten genera as case studies to establish trends in fungal description and introduce new species in each genus. The genera are the ascomycetes Colletotrichum and Pestalotiopsis (with many species or complexes), Atrocalyx, Dothiora, Lignosphaeria, Okeanomyces, Rhamphoriopsis, Thozetella, Thyrostroma (relatively poorly studied genera) and the basidiomycete genus Lepiota. We provide examples where knowledge is incomplete or lacking and suggest areas needing further research. These include (1) the need to establish what is a species, (2) the need to establish how host-specific fungi are, not in highly disturbed urban areas, but in pristine or relatively undisturbed forests, and (3) the need to establish if species in different continents, islands, countries or regions are different, or if the same fungi occur worldwide? Finally, we conclude whether we are anywhere near to flattening the curve in new species description.