bluuebunny/crossref_metadata_2025_split huggingface dataset:
Zea Mays(Maize, Corn)
Authors: Vincent P Leszek D 
Published: April 2013

AbstractZea maysL. (maize, corn) is a member of the grass family (Poaceae). It has been an important food crop since ancient times, especially among the peoples of Central and South America. Although most grasses have bisexual florets the mature florets ofZ. maysare functionally unisexual on the sample plant, a condition referred to as monoecy. The functionally male florets are borne on the tassel whereas the functionally female florets are borne on the ear. All of the components of the adultZ. maysplant are initiated within the first 4 weeks after germination. Research on maize genetics has led to some exciting discoveries (some associated with the award of a Nobel prize). These discoveries have clarified the putative origin and biology ofZ. maysand have also provided significant insights for plant biology as a whole. An overview of the taxonomy ofZ. maysis provided.Key Concepts:The species,Zea maysL. (maize/corn), is a member of the grass family (Poaceae) and a member of the genusZea. Taxonomically and nomenclaturally maize is known asZ. maysL. ssp.mays.Maize is considered to have evolved from the Mexican annual teosintes (Z. maysssp.parviglumisand ssp.mexicana).A large number of exciting genetic discoveries originated from the research on maize. One of these discoveries, the phenomenon of transposable elements, resulted in the awarding of a Nobel prize.The flowers ofZ. mays, typically referred to as florets, are initially bisexual but before the florets are reproductively functional they become unisexual, resulting in monoecy.The functionally male florets are borne terminally on the plant in the tassel. The functionally female florets are borne laterally on the plant in one or more ears.The occurrence of separate male and female florets in separate flowering structures (inflorescences) on theZ. maysplant (monoecy) has enabled the genetics of this species to be extensively studied because controlled pollinations are relatively easily performed.The morphological structure of the very young florets inZ. maysis typical of the florets in the grass family (Poaceae) in that each floret is subtended by a lemma and a palea. Pairs of florets form spikelets.In the tassel, both florets in each spikelet are functionally male and produce pollen. In the ear one of the two florets in each spikelet aborts. The remaining floret results in a kernel following successful pollination and fertilisation.
Brassicaceae (Mustard Family)
Authors: Al‐Shehbaz Ihsan A 
Published: April 2013

AbstractThe Brassicaceae (Cruciferae) or mustard family is a well‐defined group of about 310 genera and some 3500 species distributed primarily in the temperate and alpine areas of all continents except Antarctia. It is most highly diversified in central and western Asia, Mediterranean Europe and western North America. This article discusses the economic importance of the family (food, oils, condiments, ornamentals and weeds) and role played by one of its weedy member, the model organismArabidopsis thaliana, in the advancement of modern experimental biology. Here we also review the morphology, biogeography, ecology and phylogenetic relationship within Brassicaceae and to other families. We also cover the significance of molecular data in dividing the family into 48 monophyletic tribes and in determining its major lineages. Finally, a brief discussion is presented on the whole‐genome duplication events and their possible role in the radiation and diversification of the family.Key Concepts:Model organisms, such as the mustardArabidopsis thaliana, should always be used to understand complex biological phenomena in other organisms.Owing to extensive morphological convergence, molecular data alone provide the most reliable and solid phylogenetic classification within the Brassicaceae.Invasive weeds of the mustard family can only be understood by closer studies of their immediate wild relatives.Germplasm conservation centres of the economically important Brassicaceae should substantially increase their efforts to save their rapidly disappearing wild relatives.Vegetable crops ofBrassicashould be thoroughly tested to determine their medicinal values in combating cancer and other diseases.
Laurales
Authors: Renner Susanne S 
Published: April 2013

Abstract

The Laurales are an order of flowering plants comprising seven families that contain some 2500–2800 species in 100 genera. Most Laurales are tropical trees or shrubs, often with scented wood of great durability. Besides being a source of high quality timber, the Laurales also include the avocado tree (

Persea americana

), a native of Mexico and Central America, the cinnamon tree and the camphor tree (
Cinnamomum
species), native in Southeast Asia, and the bay laurel (

Laurus nobilis

), native in the Mediterranean region. The earliest lauraceous fossils are from the early Cretaceous, and within flowering plants, the order is among the oldest groups to diversify. The presently accepted classification of the seven families is based on molecular sequence data.

Key Concepts:

Many ancient groups of flowering plants are tropical trees.

Flowering plants came to dominate the World's flora during the Early Cretaceous.

Most tropical tree species have minute flowers, pollinated by bees, flies, or beetles.

Biogeographic studies of ancient tropical plant groups today usually rely on molecular clock‐based estimates of divergence times.
Dioscoreales (Yams and Allies)
Authors: Geeta R 
Published: April 2013

Abstract

Dioscoreales, the ‘true’ yams and allies, are a group whose current circumscription is dictated by results of molecular phylogenetic analyses. Consisting as it does of several nontraditional members, the group is made up of a heterogeneous set of taxa: unremarkable liliaceous plants, minute chlorophyll‐less plants that live off their associated fungal partners, and large, robust, green plants of the tropics, some of which store starch in large underground tubers (

Dioscorea

yams) that are important human food across the world, especially in Africa and the Pacific Islands. Some species are important sources of folk medicines and pharmaceuticals; the original birth pills were manufactured from relatives of the edible yams.

Dioscorea

is remarkable in the ‘dicot’‐like appearance of its stalked, net‐veined leaves borne on vines. Dioscoreales occur across the world and may existed by about 120 million years ago.

Key Concepts:

Dioscoreales are herbaceous monocots of northern temperate regions and the tropics.

Dioscoreales contain five families: Burmanniaceae, Dioscoreaceae, Nartheciaceae, Taccaceae and Thismiaceae, with 24 genera and 643 species; new species of Burmanniaceae and Thismiaceae are still being discovered.

The flower has an inferior ovary, short style and branched stigma, anthers often with apical extension. Many species contain steroidal saponins.

The order includes heterotrophs that depend on associated fungi for their nutrition (Burmannicaeae and Thismiaceae) and autotrophic tuberous plants that are a food source for other organisms including humans (Dioscoreaceae).

Dioscorea
, the genus of ‘true’ yams, contains about 10 cultivated species.

Dioscoreales are at least 123 million years old according to molecular clock estimates.
Parasitism: Life Cycle and Host Defences against Parasites
Authors: Stephen Phillips R 
Published: April 2013

AbstractParasites must reach new hosts and have evolved a variety of strategies to achieve this. For some there is a direct life cycle, with the parasite passing from one member of the host species to another via the infective stage of the life cycle. Other parasite species have more complex life cycles, known indirect life cycles, involving intermediate host species, before final transmission to the definitive host. The host's defence against parasitisation broadly takes two forms. First there are nonimmune mechanisms such as the protection given to infection with the human malaria parasitePlasmodium falciparumby the presence of the abnormal ‘sickle’ haemoglobin. Secondly, parasites can be attacked by the full panoply of the host's acquired immune defence system. A feature of most host/parasite relationships is survival of the host but equally survival of the parasite: parasites have evolved a variety of mechanisms for evading or down‐regulating the host's immune response to their advantage. The pathological consequences to the host of parasitic attack include physical damage from the host's activities to indirect consequences of the host's immune response. The problems of developing antiparasite vaccines are discussed.Key Concepts:Finding a new host is a formidable challenge for a parasite: variety of strategies evolved to achieve this end.A detailed understanding of parasite life cycles facilitates development of strategies for control of parasites of medical and veterinary importance.Host species can be very restricted for some parasites, but for some parasites many host species can be infected.Some parasites have direct simple life cycles whereas others have indirect complex lifecycles involving a vector or intermediate host.In complex life cycles the parasite's development and progression through the life cycle is adapted to the physiology and behaviour of the host.Prevalence of parasites in the host population is often over dispersed – that is most individuals have a few parasites but a few have many.In general the higher the parasite load the greater the severity of disease in the host.Defence to parasitic infection involves both nonimmune and acquired immune mechanisms.In many host/parasite relationships the host defences reduces the parasite load to low levels but fails to eliminate the parasite completely and transmission continues.Parasites have evolved a variety of strategies to survive or evade the host's defence mechanisms.
Protein–Ligand Interactions: Computational Docking
Authors: Dhanik Ankur , Kavraki Lydia E 
Published: April 2013

Abstract

A pharmaceutical drug compound is usually a small organic molecule, also termed as ligand, that binds to the target protein and alters the natural activity of the protein, thus, leading to a therapeutic effect. Computational docking or computer‐aided docking is an extremely useful tool to gain an understanding of protein–ligand interactions which is important for the drug discovery. Computational docking is the process of computationally predicting the placement and binding affinity of the ligand in the binding pocket of the protein. Docking methods rely on a search algorithm which computes the placement of the ligand in the binding pocket and a scoring function which estimates the binding affinity, that is, how strongly the ligand interacts with the protein. A variety of methods have been developed to solve the computational docking problems that range from simple point‐matching algorithms to explicit physical simulation methods.

Key Concepts:

Computational docking methods play an important role in the drug discovery process.

A docking method computes the placement of a ligand in the binding pocket of a protein and estimates the binding affinity.

Rigid‐body docking methods treat both the protein and ligand as rigid bodies.

Flexible ligand methods treat the ligand as a flexible molecule and flexible receptor methods treat both the ligand and the protein as flexible molecules.

Two main features of computational docking techniques are a conformation search algorithm and a scoring function that estimates binding affinity.

Most of the computational docking programs treat the protein as a rigid molecule and the ligand as a flexible molecule.

Protein flexibility is an important determinant of the accuracy of docking programs.

Efforts have been made to account for protein flexibility in docking methods, but more needs to be done.
Isochores
Authors: Bernardi Giorgio 
Published: April 2013

Abstract

Chromosomes of warm‐blooded vertebrates are mosaics of isochores, megabase
deoxyribonucleic acid
(DNA) stretches that are fairly homogeneous in base composition. In the human genome, isochores can be assigned to five families that cover a very broad range of guanine+cytosine (30–60% GC; this range is narrower in cold‐blooded vertebrates). The isochore structure of the genome led to new insights into a number of important genome features such as (1) the distribution of genes, (2) the structure of chromatin, and (3) the localisation of insertions/deletions and of the integration of proviral sequences. Moreover it also led to (1) the discovery of a set of correlations (collectively called the genomic code) linking coding sequences and extended flanking noncoding sequences, as well as other genome features, (2) the visualisation of the isochore patterns of the genomes as genome phenotypes, that may be conserved or change in evolution, like the classical phenotypes, and (3) the development of the neoselectionist theory of evolution, which explains the two modes, conservative and shifting, of genome evolution.

Key Concepts:

Isochores are the structural, functional and evolutionary units of the genomes of vertebrates and other eukaryotes.

Structurally, isochores correspond to the highest resolution bands of chromosomes.

Functionally, isochores from different families are characterised by different frequencies of short oligonucleotides, not only in the extended inter‐ and intragenic noncoding sequences, but also in short regulatory sequences upstream and downstream of coding sequences. Moreover, different categories of genes have a different distribution in isochore families.

Evolutionarily, the isochore patterns change in different classes of vertebrates, from the relatively simple (low‐heterogeneity) patterns of cold‐blooded vertebrates to the complex (high‐heterogeneity) of warm‐blooded vertebrates.
Titin Gene (

TTN

)
Authors: Labeit Siegfried , Bogomolovas Julius , Labeit Dietmar , Granzier Henk 
Published: April 2013

Abstract

The titin locus located on chromosome 2q24 in the human genome expresses about 100 kb full‐length mRNAs, that are translated into giant up to 34.350‐residue large polypeptides. Therefore, titin is by far the largest known protein. The titin protein is abundant in vertebrate muscles, where it spans half of the sarcomere.

In situ

, 1–2 μm long titin polypeptides establish a sarcomeric filament system that is critical for myofibrillar integrity and elasticity. Biomechanically, titin's intrinsic elasticity is fine‐tuned in the different muscle tissues through alternative splicing, post‐translational modifications and protein–protein interactions. Moreover, a plethora of molecular interactions with stress‐regulated ligands positions titin centrally in stretch‐dependent signalling in muscle. Therefore, mutations in this filament system are important causes of hereditary cardiomyopathies and muscular dystrophies.

Key Concepts:

Sarcomeres consist of precisely assembled proteins that together form the basic functional units of striated muscle and give rise to efficient and finely tuned contraction.

In muscle tissues, 1–2 μm single titin polypeptide chains span half of the sarcomere.

The intrasarcomeric filamentous titin protein provides sarcomeres with intrinsic elasticity and couples stretch‐dependent signalling together with muscle remodelling.

Titin molecule is tailored to physiological requirements of different muscles through alternative splicing, post‐translational modifications and protein–protein interactions.

Mutations in the titin gene are associated with different heart and skeletal muscle diseases.
Alternative Processing: Neuronal Nitric Oxide Synthase
Authors: Marsden Philip A , Newton Derek C , Tsui Albert K Y 
Published: April 2013

AbstractThe humanneuronal nitric oxide synthase(nNOS) gene is expressed from multiple promoters and is subject to alternate messengerribonucleic acid(mRNA) processing. These complex molecular mechanisms contribute to regulating gene expression and function in multiple tissues and cell types. In the case of nNOS, these distinct promoters give rise to mRNA transcripts with untranslated leader sequences that have differing lengths, nucleotide composition and three‐dimensional structure. These distinct leader sequences have robust effects on translational efficiency. In disease settings, these have functional relevance. For example, in settings of low oxygen content, a unique promoter becomes trancriptionally active. In contrast to basally expressed transcripts, this hypoxia‐induced mRNA is very efficiently translated. To accommodate diverse biological roles, multiple mechanisms have evolved to produce a diverse range of nNOS mRNA transcripts from a single genetic locus.Key Concepts:Mammalian genes can have more than one promoter.Having more than one promoter implies that the gene has more than one version of exon 1.Initiation of transcription in different regions of genomic DNA imparts different nucleotide sequences to the leader regions of messenger ribonucleic acid transcripts, also known as the 5′‐untranslated region (5′‐UTR).Different leader sequences may, or may not, affect protein structure depending on whether the initiator AUG codon for translation of the protein lies in exon 1 or downstream.If multiple versions of exon 1 all have their own initiator AUG codon, then the encoded protein will exist if different forms, each with a uniqueN‐terminal peptide sequence.Different 5′‐UTRs of messenger ribonucleic acid transcripts can have functional effects on expression of the encoded protein.The 5′‐UTRs of messenger ribonucleic acid transcripts can affect translational efficiency.The 5′‐UTRs of messenger ribonucleic acid transcripts can affect subcellular messenger ribonucleic acid transcript localisation.The 5′‐UTRs of messenger ribonucleic acid transcripts can affect messenger ribonucleic acid transcript stability.
t
RNA
and the Human Genome
Authors: Goldman Emanuel 
Published: April 2013

Abstract

Transfer
ribonucleic acid
(tRNAs) decode the genetic code and carry attached amino acids to the growing protein chain on the ribosome. With the availability of the complete sequence of the human genome, at least 497 tRNA genes have been identified (which include some gene duplications). With the exception of the UGA‐decoding tRNA that inserts selenocysteine into protein under special circumstances, no tRNAs were found that decode stop codons. This opens up the possibility of using nonsense codons for insertion of nonnatural amino acids into selected proteins, to facilitate structural and functional analyses of these proteins. This has been accomplished by evolving tRNA:aminoacyl‐tRNA synthetase pairs in which the synthetase recognises a nonnatural amino acid and attaches it to its partner nonsense‐suppressor tRNA and no other tRNAs.

Key Concepts:

tRNAs are grouped into families of isoacceptors, with each family recognised by a single cognate aminoacyl‐tRNA synthetase.

All tRNAs conform to a secondary structure described as a ‘cloverleaf’, and fold in three‐dimensional space into an ‘L‐shaped’ molecule, in which the amino acid and the anticodon are at opposite ends of the molecule.

The 3′ end of all tRNAs have the sequence CCA, with the amino acid attached by the tRNA synthetase to the terminal adenosine residue. In eukaryotic cells, the 3′ terminal CCA is not encoded but is enzymatically added posttranscriptionally.

The anticodon of the tRNA decodes a complementary codon on mRNA in an antiparallel fashion.

Wobble between the third codon position in an mRNA and the first anticodon position in the tRNA extends allowable base‐pairing.

There are extensive modifications of the bases in tRNAs, with functional importance.

During protein synthesis, tRNAs interact with the ribosomal ‘A’ (aminoacyl), ‘P’ (peptidyl) and ‘E’ (exit) sites.

All organisms exhibit preferred ‘codon bias’, in which certain synonymous codons are preferred over others, generally corresponding to cognate tRNA abundance.

The human genome has 497 identified tRNA genes and 324 putative tRNA pseudogenes. There are no tRNAs that decode stop codons.

Dedicated, unique tRNA: aminoacyl‐tRNA synthetase pairs have been developed for insertion of nonnatural amino acids into protein.
Transmembrane Domains
Authors: Ramasarma T , Joshi NV , Sekar K , Uthayakumar M , Sherlin D 
Published: April 2013

AbstractStretches of approximately 25 hydrophobic residues with an occasional polar residue of integral proteins that pass across membrane are known as transmembrane (TM) domains. Besides anchoring to the membrane they participate in the functions of these proteins in some unspecified way. A variety of membrane proteins with spans in the range 1–17 are present in human genome and those with 1, 4 and 7 spans are more common. Impacting a variety of cellular functions, these include receptors for growth factors, hormones and other ligands, two‐way membrane transporters, selective enzymes, channel proteins, energy‐transducing tiny molecular motor, molecular facilitators in signalling, adhesion, differentiation and proliferation. Highly variable sequences of these short stretches of hydrophobic residues of TM domains, with hardly any repetition, arise out of repeating XTX/XCX triplets in theircomplementary deoxyribonucleic acid (cDNA). They are encoded by a random exon make‐up, one exon coding for one or more domains and one domain coded by two exons with the junction between triplets and in some cases within a triplet.Key Concepts:Cell membrane is composed of hydrophobic phospholipid bilayer that separates two aqueous phases.The selective permeability endows the membrane two‐way transport of desired materials.Proteins attached to the membrane facilitate this exchange process.Proteins that span across the bilayer in one or multiple passes are known as integral proteins or transmembrane (TM) proteins.TM domains, composed of largely hydrophobic residues, anchor these proteins firmly to the membrane and also participate in the functions.Topology of TM domains facilitates transfer of signals, channelling ions and transporting material.The amino acid sequences of TM domains are highly variable and are not repeated.Some of these short stretches of TM domains are encoded by two exons with junction between triplet or within triplet.