bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple Aromaticity, Multiple Antiaromaticity, and Conflicting Aromaticity in Inorganic Systems
Authors: Zubarev Dmitry Yu. , Boldyrev Alexander I. 
Published: September 2009

Abstract
In recent years there have been significant advances in extending the concepts of aromaticity and antiaromaticity into the realm of inorganic chemistry. These new developments have shown that aromaticity and antiaromaticity in metal systems are frequently multiple in nature. Two new types of aromaticity, namely, δ‐ and ϕ‐aromaticity, were found in transition metal and f‐element cyclic systems in addition to the σ‐ and π‐types already known in organic chemistry. There are also now many examples of inorganic systems with conflicting aromaticity, which refers to the systems with simultaneous presence of aromaticity and antiaromaticity in different electronic (σ‐, π‐, δ‐, or ϕ‐) subsystems. It was shown that the antiaromaticity in any electronic subsystem could be interpreted in terms of formation of small areas of aromaticity leading to the island aromaticity.
Computational Studies: Boranes
Authors: Shameema Oottikkal , Jemmis Eluvathingal D. 
Published: September 2009

Abstract

Computational studies on boranes, in recent years, are summarized with the special emphasis on the macropolyhedral boranes. Computational studies to understand the energetics, geometry, aromaticity, and reactivity of boranes and substituted boranes are reviewed. There is a recent interest in macropolyhedral boranes because of their uses in boron neutron capture therapy (BNCT) of cancer, ionic liquids, weakly coordinating ions, and materials chemistry. The
mno
rule, which is the electronic counting rule for the macropolyhedral boranes, is explained. Even though the electron counting rule explains the electronic structure of macropolyhedra, it cannot explain the relative stability of isomers since different structures are possible with the same electron count. There have been many computational studies to explain the relative stability of various structural patterns in macropolyhedral boranes. We have used the concept of orbital compatibility to explain the relative energies of different macropolyhedral structural patterns. Computations on the
closo
‐
closo
macropolyhedral boranes show that a large polyhedral borane prefers to condense with a smaller polyhedron owing orbital compatibility. Even though only a few
closo
‐
closo
macropolyhedral structures have been synthesized experimentally, calculations suggest optimism for the synthesis of many condensation products. A brief discussion about the use of the computational methods for the rearrangement of the B
20
H
16
skeleton reacting with ligands is also provided.
Nuclear Magnetic Resonance (NMR) Parameters of Transition Metal Complexes: Methods and Applications
Authors: Kaupp Martin , Bühl Michael 
Published: September 2009

AbstractThis article provides an overview of first‐principle computations targeted at nuclear magnetic resonance (NMR) properties of transition‐metal complexes. Recent methodological developments and illustrative applications are highlighted, all of which are rooted in density functional theory (DFT). Special attention is called to chemical applications of such NMR computations, ranging from structure elucidation of metalloenzymes to detailed interpretation of NMR spectra of paramagnetic compounds.
Computational Methods: Transition Metal Clusters
Authors: Gautier Régis , Halet Jean‐François , Saillard Jean‐Yves 
Published: September 2009

AbstractCluster chemistry is dominated by structural aspects. Indeed, structure and bonding are strongly related to stability and properties, and cluster structures are particularly diverse and often complex. Thus, electron‐counting rules, which relate structure to electron count, have been the key to the development of cluster chemistry as a distinct area of chemistry. These rules have been set up progressively along time with the help of quantum chemistry. This article deals with the recent progress on transition metal and mixed main group/transition metal cluster chemistry arising from the contribution of modern computational theory to the rationalization of structures. This article focuses on “viable” species, i.e., molecules that are isolable under reasonable conditions and deals with the exploration of the limitations of the classical electron‐counting rules as well as the establishment of new rules for new structural types with the help of quantum chemical calculations.
Computational Studies: Chemical Evolution of Metal Sites
Authors: Jensen Kasper P. 
Published: September 2009

Abstract

The structures of naturally occurring metal sites have evolved over hundreds of millions of years to perform complex functions under very specific biological and nonbiological constraints. Modern computational chemistry has now reached a level of accuracy that allows us to study the full significance of molecular evolution by systematically altering the components of the native metal sites and by monitoring the resulting effects on relevant computed properties. This procedure, referred to as
computational chemical evolution
, not only explains the use of certain metal ions as opposed to others in metalloproteins, but also lends promise to the design of new multifunctional metal sites that are no longer restricted by biological constraints, to be used in medicine and catalysis.
Theoretical Aspects of Main Group Multiple Bonded Systems
Authors: Silaghi‐Dumitrescu Ioan , Petrar Petronela , Nemeş Gabriela , Bruce King R. 
Published: September 2009

Abstract

Computational data on homonuclear multiple bonding between elements of group 13 and heavier elements of group 14 are reviewed. For R

n

EER

n

, there is an increased tendency of bending the RER planes (
n
= 2) or the RE bonds (
n
= 1) toward the EE axis upon descending a group. This is related to the mixing of the valence σ–π orbitals reflecting the tendency of the heavier elements to retain nonbonding character for their
n
s
2
orbital. As a result, the bond orders are also reduced and the EE interaction weakened.
Basal Ganglia and The Regulation of Movement
Authors: Turner Robert S 
Published: September 2009

Abstract

The basal ganglia (BG) is composed of several heavily interconnected nuclei at the base of the cerebrum. A series of anatomically distinct parallel circuits through the BG receive afferent projections from and project back to cortical regions that mediate skeletomotor, oculomotor, frontal associative, and limbic functions. All circuits share a common intrinsic organization captured largely by the heuristic model of direct and indirect pathways that link BG input stations to outputs. Activation of the direct pathway may facilitate movement whereas the indirect pathway may suppress movement. Neuromodulators such as dopamine have different effects on activity and synaptic plasticity in the two pathways. Clinical disorders that involve the BG are often associated with movement disorders. Although the actual roles of the BG in the control of movement are still actively debated, growing evidence suggests it acts as a reinforcement‐driven tutor for learning automatic behavioural routines.

Key concepts

The BG is organized as anatomically segregated loop circuits that contribute to the control of movement, cognition and motivation.

All BG circuits share a common basic organization.

Input projections from cortex and thalamus terminate as excitatory synapses in the striatum and subthalamic nucleus.

Output projections tonically inhibit target neurons in thalamic and brainstem nuclei.

Direct and indirect pathways connect input and output nuclei of the BG.

Activation of the direct pathway facilitates movement whereas activation of the indirect pathway suppresses movement.

A variety of neuromodulators, such as dopamine, affect the activity of neurons in the direct and indirect pathways differently.

Most BG‐related clinical conditions (e.g. Parkinson disease) arise from imbalanced activation of direct and indirect pathways and involve abnormal discharge patterns in BG output neurons.

BG circuits may regulate how an animal allocates time and effort to movements and actions and act as a tutor for new skill learning.
Oncogenic Viruses
Authors: McCance Dennis John 
Published: September 2009

Abstract
Infectious agents account for appropriately 25% of cancers worldwide and viruses in particular have been useful in elucidating many of the cellular pathways that can be deregulated in cancer. Therefore, the more that is known about how viral proteins disrupt the normal cell the more we will learn about important regulatory pathways that when altered or abrogated, lead to a transformed cell.
Phylogeny Based on 16
S
r
RNA
/
DNA
Authors: Stackebrandt Erko 
Published: September 2009

Abstract

Polyphasic systematics of prokaryotes is guided by the results of comparative analysis of the evolutionary conservative 16S ribosomal
ribonucleic acid
(RNA) genes. Certain genes coding for ‘housekeeping’ proteins support the phylogenetic outline but most of these genes are either not ubiquitous or they are evolving too rapidly to embrace all higher taxa. Dendrograms of phylogenetic relatedness show the order at which organisms evolved in time, thus providing the frame for their classification. The delineation and circumscription of taxa should not be solely based on the topology of dendrograms but it is advised to include a wide range of molecular, chemical and metabolic properties, which need to be assessed and evaluated in the light of novel taxonomic information.

Key concepts:

The results of comparative 16S ribosomal
ribonucleic acid
(rRNA) gene sequence analysis shattered the dogma of the bifurcation of higher life form categories, that is prokaryotes versus eukaryotes.

The advantage of rRNA genes over genes coding for proteins is a combination of properties: universal presence, easy accessibility and polymerase chain reaction (PCR) amplification, rare lateral gene transfer and broad coverage of taxa between domain and species.

The only taxonomic category where the 16S rRNA gene sequence fails to unravel detailed evolutionary insights into the structure of its members is the taxon ‘species’.

Taxonomy of a strain is more than the analysis of a few sequences: it is a pragmatic concept that takes into account the results of its evolutionary history leading to changes at the genomic, epigenetic and phenotypic levels.

Classification is a process in which the database of a strain is compared to the network of strains already classified. Its place in the system is found when this dataset matches most closely the dataset of an already classified taxon. In this process the 16S rRNA sequence guides the affiliation to the genus level.
Antigens: Thymus‐dependent
Authors: Bachmann Martin F 
Published: September 2009

AbstractB cells secrete antibodies that mediate protection against a great variety of pathogens. There are two classes of antigens for B cells, T cell‐dependent (thymus‐dependent, TD) and T cell‐independent (TI) antigens. The former require the presence of cognate T‐helper (TH) cells to trigger a B‐cell response, whereas the TI antigens can mount an antibody response in the absence of TH. A large class of antigens, namely proteins on pathogen surfaces, are both TI and TD: They are able to induce a TI IgM (immunoglobulin M) antibody response, since they are highly repetitive and linked to toll‐like receptor (TLR) ligands and they induce a TD response, since they are proteins. Epitope repetitiveness, presence of TLR‐ligands and T help together shape the quantity, quality and duration of an antibody response.Key Concepts:TI antigens induce antibody responses in the absence of TH.TI antibody responses are mostly of the IgM isotype and short‐lived.TD antigens require THcells to induce an antibody responses.TD antibody responses are usually of the IgG isotype and more long‐lived.Pathogens are complex antigens and are both TI (they are repetitive and contain TLR ligands) and TD (they contain proteins and induce TH).This combination of TI and TD makes pathogens such strong immunogens for B cells.Antigen‐repetitiveness and presence of TLR ligands modulate the overall magnitude of the antibody responses.Presence of THimprints memory into the antibody responses by allowing the formation of long‐lived plasma cells as well as memory B cells.
Epitopes
Authors: Muller Claude P , Jacoby Monique 
Published: September 2009

AbstractT‐ and B‐cell epitopes differ fundamentally in the way they are recognized by the immune system. B‐cell epitopes are recognized as three‐dimensional structures on the surface of native antigens. T‐cell epitopes are parts of internalized and processed antigens that are presented to T lymphocytes in association with molecules of the major histocompatibility complex. Since in a biological system T‐ and B‐cell receptors or antibody molecules face a virtual infinite number of structures, cognate interactions with epitopes are the basis of the primordial intelligence that drives the teleological choices of the immune system. Although theoretically any antigen comprises a myriad of potential epitopes, the immune response will focus only on a few of them by a phenomenon termed immunodominance. Understanding the mechanisms that govern epitope selection is important for epitope prediction and vaccine design.Key conceptsSurface immunoglobulins of B cells and antibodies recognize the B‐cell epitope of an antigen in its native conformation.The main common feature of B‐cell epitopes (BCEs) is accessibility on the surface of the antigen.T‐cell receptors (TCRs) recognize the T‐cell epitopes (TCEs) only after intracellular processing of the antigen, and in association with major histocompatibility complex (MHC) molecules, a concept termed MHC restriction.TCEs presented by MHC class II molecules are longer and more variable in size than those presented by MHC class I molecules.TCE peptides that bind to the same allele of MHC class I molecules share common ‘anchor’ residues that contact the MHC molecule. In MHC class II‐restricted TCEs, the anchor residues are less well defined.High affinity of the TCR–MHC–peptide tripartite interaction as well as coreceptors and other signalling modules are needed for T‐cell activation.Immunodominance refers to the concept that only a small subset of the potential epitopes (TCEs or BCEs) present in a given antigen elicit an immune response.The immunodominance of a TCE depends on its accessibility within the antigen, the specificity of processing enzymes and its affinity to transporter proteins, chaperons, MHC and TCRs.Mimotopes are small molecules that mimic the structure of complex conformational epitopes without any sequence homology.
Transfer
RNA
Recognition by Synthetases
Authors: Giegé Richard , Eriani Gilbert 
Published: September 2009

Abstract

Fidelity of transfer
ribonucleic acid
(tRNA) charging by amino acids ensures correct translation of the genetic code into proteins. Charging is catalysed by a set of enzymes known as aminoacyl‐tRNA synthetases. Owing to the degeneracy of the genetic code, some of the different tRNAs have the same amino acid attached to them. Specificity of the charging reaction is ensured by positive elements, the identity determinants unique to each tRNA and responsible for its recognition by the cognate synthetase, and negative elements, the antideterminants that prevent false recognitions. To fulfil the aminoacylation specificity and prevent noncognate aminoacyl‐tRNA delivery to the ribosome, some synthetases also mediate proofreading reactions that increase fidelity of the tRNA charging. In such reactions, misactivated amino acids or mischarged tRNAs are checked in specific sites and noncognate products are hydrolysed.
Translation Initiation Models in Prokaryotes and Eukaryotes
Authors: Londei Paola 
Published: September 2009

Abstract

Translation is one stage of protein synthesis in which messenger
ribonucleic acid
(mRNA) acts as a template for the synthesis of a polypeptide chain; it consists of four phases: initiation, elongation, termination and ribosome recycling. Initiation of protein synthesis, entailing ribosomal recognition of the mRNA start codon and the setting of the correct reading frame, is the rate‐limiting step of translation and the main target of translation regulation in all cells. However, the mechanism and molecular machinery for initiation have diverged in the primary domains of life: the Bacteria, the Archaea and the Eukarya (eukaryotes). In bacteria, translation initiation is relatively simple, while in eukaryotes is complex and requires more components. In archaea, despite their prokaryotic phenotype, the machinery for protein synthesis initiation is much more elaborated than in bacteria and presents intriguing similarities with the corresponding eukaryotic process. The features of translational initiation in archaea, bacteria and eukaryotes are reviewed, highlighting the divergent and common aspects of this important cellular process in the three domains of life.

Key concepts

Initiation is the first of four steps of the translation cycle. During initiation the small ribosomal subunit interacts with the messenger
ribonucleic acid
(mRNA) and finds the right start codon, thereby setting the correct reading frame for decoding.

In all cells, translation initiation is assisted and modulated by several proteins called translation initiation factors (IFs). The most important roles of the IFs are to select the proper initiator transfer RNA, to adjust it correctly in the ribosomal P site, to ensure the accurate selection of the start codon and to prevent the premature joining of the large ribosomal subunit to the pre‐initiation complex.

Initiation is the rate‐limiting step of translation. It is the efficiency whereby an mRNA is decoded and the amount of final product is largely determined at the initiation level.

In all cells, the principal mechanisms of translational control act at the level of initiation, usually targeting certain IFs that play essential roles in the initiation process.

The initiation step of translation has incurred a marked evolutionary divergence. The mechanism and components of initiation differ in several aspects in the three primary domains of life, that is the Bacteria, the Archaea and the Eukaryotes.

The Bacteria have the simplest machinery for translation initiation. However, this is not because they are prokaryotes. The other prokaryotic domain, the Archaea, has a fairly complex machinery for initiation, resembling that of eukaryotes, which have the most complex initiation process.
Inhibitors of the Elongation Cycle of Protein Synthesis
Authors: Wilson Daniel N , Starosta Agata L , Yamamoto Hiroshi , Nierhaus Knud H 
Published: September 2009

Abstract

The protein synthetic machinery is a highly complex apparatus that offers many potential sites for functional interference and represents a major target in the cell for antibiotics. The knowledge of ribosomal structure and function has progressed enormously in recent years, which has, in turn, accelerated our understanding of the mechanism of drug action. Conversely, drugs have been used as tools to probe the translation cycle, thus providing a means to further dissect the multitude of steps involved in protein synthesis. In an era where bacteria are showing an ever‐increasing resistance to many clinically relevant antibiotics, the importance of understanding their mechanism of inhibition is essential to the development of novel and more effective replacements.

Key concept:

A large number of antibiotics target the ribosome and inhibit specific steps during the elongation cycle.
Ribosomal Proteins: Role in Ribosomal Functions
Authors: Wilson Daniel N , Gupta Romi , Mikolajka Aleksandra , Nierhaus Knud H 
Published: September 2009

Abstract

The assignment of specific ribosomal functions to individual ribosomal proteins is difficult due to the enormous cooperativity of the ribosome; however, important roles for distinct ribosomal proteins are becoming evident. Although ribosomal
ribonucleic acid
(rRNA) has the major claim to certain aspects of ribosome function, such as decoding and
peptidyltransferase
activity, there are also protein‐dominated functional hot‐spots on the ribosome such as the messenger RNA (mRNA) entry pore, the translation factor‐binding site and the exit of the ribosomal tunnel. The latter is binding site for both chaperones and complexes associated with protein transport through membranes. Furthermore, the contribution of ribosomal proteins is essential for the assembly and optimal functioning of the ribosome.

Key concepts:
Both the 16S and 23S rRNAs and a subset of r‐proteins are essential for assembly, structure and function of ribosomes; the ribosomal interface, the place where the three tRNA‐binding sites A, P and E are located and thus where protein synthesis occurs, is preferentially composed of rRNA; functional hot‐spots such as mRNA entry pore, elongation factor‐binding site (L7/L12 stalk), the L1 protuberance and the tunnel exit are dominated by r‐proteins; many r‐proteins have a globular domain and long extensions protruding deep into the ribosome; the globular domains of r‐proteins are located at or near the ribosomal surface; antibiotic resistance can be mediated by mutations in either rRNA or r‐protein genes; some r‐proteins are essential for assembly but play no role in structure or function of the ribosome; accuracy of proteins is tuned and balanced by r‐proteins (S4, S5 and S12); r‐proteins at the tunnel exit can function as a docking station for factors important for protein folding or for attaching the ribosome to membranes.
Bacterial Flagella: Flagellar Motor
Authors: Wadhams George H , Sowa Yoshiyuki 
Published: September 2009

Abstract

The bacterial flagellar motor is a complex biological rotary molecular motor which is situated in the cell envelopes of bacteria. Whereas most biological motors use adenosine triphosphate (ATP) as their energy source, the rotation of the flagellar motor is driven by a flow of charged ions across the bacterial plasma membrane. The motor powers the rotation of helical flagellar filaments at speeds of up to several hundred hertz. These rotating filaments act like propellers, pushing the cells through their environment. The motors are regulated by one of the best‐characterized biological signalling pathways, the chemotaxis pathway. This pathway changes the swimming pattern of the bacteria in response to changes in the concentration of external chemicals so that they move into environments which are optimal for their growth.

Key concepts:

Bacteria swim using a small biological rotary motor which is powered by the movement of charged ions across the plasma membrane.

The flagellar motor consists of a rotor which rotates against stator units that are anchored to the peptidoglycan cell wall.

Torque is generated by the interaction of the stator units, MotA and MotB, with FliG in the rotor.

Despite the fact that the driving ions always flow in one direction through the stator units, many flagellar motors can switch between clockwise and counterclockwise rotation.

A complex signalling pathway regulates the motor output in response to environmental signals ensuring that bacteria swim towards nutrient rich environments.