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The article discusses the unidentified factors that caused the nitrogen (N)[2]) loss in the oceans. According to oceanographers it was virtually caused by denitrification, while investigators in the Netherlands, Germany and Denmark have revealed an additional biochemical called ammonia oxidation or anammox that produces N[2] in ocean waters. Meanwhile, Europeans showed that annamox in the absence of denitrification, accounted for most N[2] generation.

The article reports on the research conducted by David Bartel and Nikolaus Rajewsky regarding the implication of RNA to the production of cellular proteins in the U.S. When both intellectuals presented their work during the molecular biology symposium in Miami, they discovered that they were tackling the same issue. To unveil the mystery behind these cellular proteins, they need to look at changes in thousands of proteins at once and detect the differences in protein abundance. They found a glean insight into how miRNA act to fine tune the levels of thousands of proteins in a cell.

The article provides information on a study about the calcium sensor approach that allows rapid and sensitive tracking of localized calcium signals with high temporal and spatial resolution. The researchers have presented a combination of tunability and small size of synthetic chemical indicators with the spatial resolution and control of genetically targeted proteins. Furthermore, they have developed a prototype small-molecule sensor, known as Calcium Green FlAsH in which it is comprised of receptor that binds selectively to calcium. Meanwhile, the author concludes that the researchers' general concept could be used to visualize protein regions by using methods other than fluorescence.

Evolution by natural selection peerlessly describes how life's complexity develops — but can it be explained in terms of physics? A new approach suggests it can. Radical theory explains how physics creates all biology's complexity. [ABSTRACT FROM AUTHOR]

The story of how the structure of DNA was found is one of team science from which one member was unforgivably excluded. [ABSTRACT FROM AUTHOR]

The protein NINJ1 drives membrane rupture associated with certain types of cell death. Investigation of NINJ1 reveals mechanistic details of how it functions, raising the possibility of developing new therapeutics.Insights into a mechanism that ruptures the plasma membrane. [ABSTRACT FROM AUTHOR]

An unusual form of cell death called ferroptosis can sweep over embryonic tissues in a wave-like manner to ensure proper muscle development — evidence that ferroptosis has a role in normal physiology.Iron-dependent cell death sweeps across tissue to shape embryonic muscle. [ABSTRACT FROM AUTHOR]

High-resolution structures of TAAR1 — the receptor bound by amphetamines and molecules called trace amines — reveal detailed interactions with ligand molecules that will inform efforts to design antipsychotic drugs. Insight into how ligand molecules bind to the TAAR1 receptor. [ABSTRACT FROM AUTHOR]

Proteins spanning the membranes of cells of the intestine and kidney use sodium-ion gradients to take up glucose, enabling water absorption, too. The structures of these transporter proteins have now been observed in detail.Human sodium-coupled glucose transporters seen in detail. [ABSTRACT FROM AUTHOR]

How do mitochondrial organelles remove damaged parts of inner membrane for recycling in the cytoplasm? The discovery of an exit route that flips inner membrane outside the organelle provides some answers. Pathway selectively removes inner membrane from mitochondrial organelles. [ABSTRACT FROM AUTHOR]

Proteins have been designed that assemble in different ways depending on whether an ‘effector’ molecule is present — a demonstration of allostery, the phenomenon that enables switch-like control of protein functions in nature.Designer proteins that exhibit the phenomenon of allostery. [ABSTRACT FROM AUTHOR]

Precursor messenger RNA is edited into its final form by an RNA–protein assembly called the spliceosome. Structural evidence provides insights into how the spliceosome is disassembled when its job is complete.Structural evidence reveals key steps during spliceosome disassembly. [ABSTRACT FROM AUTHOR]

As a tech-hungry world gobbles up rare-earth elements, researchers are adapting bacteria that can isolate and purify the metals in the absence of harsh chemicals. [ABSTRACT FROM AUTHOR]

The discovery of bacterial compounds that have antifungal properties opens up opportunities for the development of agents that protect crops from a devastating disease.Natural products that protect plants from a common disease. [ABSTRACT FROM AUTHOR]

The Chilean soapbark tree is the source of QS-21 — a valuable but hard-to-obtain vaccine additive. Yeast strains engineered to express all components of the QS-21 biosynthetic pathway provide an alternative route to this therapeutic.Engineered yeast recreate synthesis pathway of medicinal plant extract. [ABSTRACT FROM AUTHOR]

Arising from S. Pawar, A. I. Dell & V. M. Savage 486, 485-489 10.1038/nature11131(2012)A recent paper by Pawar and colleagues has provided important insights into the consequences of foraging behaviour for food-web dynamics. One notable pattern predicted by their analysis is that consumption rate (c) scales superlinearly (cm1.16) with consumer body mass (m) in three-dimensional (3D), but not two-dimensional (2D), foraging spaces. Although we feel that the authors should be applauded for this interesting contribution, we argue that their result is not consistent with established life-history theory. To resolve this contradiction, progress in both fields is probably required, including new empirical studies in which consumption rate, metabolism and dimensionality are examined directly under natural conditions. [ABSTRACT FROM AUTHOR]

The enzymatic pathway has been characterized for the production of ketocarotenoids: the red pigment in some birds' feathers and in eye cells that detect red light. Red pigment in birds and fish is produced by a two-enzyme pathway. [ABSTRACT FROM AUTHOR]

By modifying the blueprint of life, researchers are endowing proteins with chemistries they’ve never had before. [ABSTRACT FROM AUTHOR]

A newly discovered fossil record of steroid molecules, spanning 1.64 billion years, points to ancient organisms in the eukaryotic domain being capable of only early steps in the synthesis of sterol molecules.Analysis of molecular fossils sheds light on how sterol pathways evolved. [ABSTRACT FROM AUTHOR]

Proteins can condense to form membraneless organelles, which act as vessels for biochemical reactions in cells. An investigation shows that protein condensation is also a cellular mechanism for controlling water availability. A rapid cellular response to thermal and osmotic shocks. [ABSTRACT FROM AUTHOR]

Collaborations between AI researchers and China’s medical workers are helping to combat diseases such as diabetes and COVID-19. [ABSTRACT FROM AUTHOR]

Light-sensitive proteins called rhodopsins in the vertebrate eye initiate the cellular processes of vision. Leading-edge crystallography experiments have revealed the molecular mechanism by which light activates these proteins.Snapshots of pigment isomerization in the rhodopsin protein. [ABSTRACT FROM AUTHOR]

The article presents an analysis of the paper in the Journal of Biological Chemistry which examined signaling pathways in the development of skin cancer. This journal retracted the paper after an investigation prompted by an anonymous electronic mail. With this, the authors were told that the paper contained data that was reproduced without citation and with different labeling from a paper the same group had published in 2004.

The article focuses on the contributions of Shuya Fukai who is an associate professor at the Tokyo Institute of Technology. He has developed techniques to help other scientists better determine three-dimensional protein structures, particularly for protein-RNA complexes. The work has produced clear snapshots of a three-step chemical reaction. It was stated that Fukai's expertise in crystallography, biochemistry, and molecular biology made solving these structures possible.

A metallochaperone protein that ensures that zinc ions are delivered to a crucial cellular enzyme has now been discovered. The finding underscores the subtleties of controlling cellular zinc allocation when the metal is scarce. Zng1 is an evolutionary conserved chaperone protein for zinc ions. [ABSTRACT FROM AUTHOR]

It is textbook knowledge that some bacteria can generate methane enzymatically. A study now provides evidence that an alternative, non-enzymatic mode of methane production could occur in all metabolically active cells.Non-enzymatic methane production in metabolically active cells. [ABSTRACT FROM AUTHOR]

A microorganism that dwells in an underground oil reservoir has been found to degrade various petroleum compounds and use them to produce methane through a previously unreported biochemical pathway.A microorganism in an oil reservoir produces methane from hydrocarbons. [ABSTRACT FROM AUTHOR]

The article reports on the study conducted by researchers Irene Stemmler and Gerhard Lammel of the Max Planck Institute for Chemistry regarding the environmental effects of dichlorodiphenyltrichloroethane (DDT) in Mainz, Germany. The researchers found that DDT may have accumulated in large amounts to oversaturate the surface waters and be re-emitted into the atmosphere. Using a three-dimensional atmosphere-ocean global circulation model, the researchers found that the western North Atlantic ocean has been re-emitting DDT for more than three decades, longer that most other regions. They also suggests that the distribution of the pesticide has been creeping northwards.

The article reports on development related to research. Researchers from the University of Bonn showed that inhibiting cannabinoid receptors either genetically or chemically enhances skin hypersensitivity to allergens in mice. Meanwhile, researchers at the University of Texas analyzed 133 samples of yellow fever virus to examine RNA sequences. A team at the European Molecular Biology Laboratory showed that transcription factor called Bsx regulates the level of spontaneous physical activity.

Focuses on papers in this issue, which provide insights into the biochemical features of a molecular mechanism which establishes spatial boundaries in developing tissues. Attachment of carbohydrate chains to a receptor on the cell surface which can modulate the interaction of the receptor with its binding partners; Location of glycosylation of the receptor Notch by the protein Fringe.

Molecular crosslinks known as disulfides stabilize the 3D structures of many proteins, and sometimes regulate protein function. But disulfides are not alone — another type of regulatory protein crosslink has been discovered.A covalent linkage between cysteine and lysine residues in a protein. [ABSTRACT FROM AUTHOR]

Peptidoglycan (PG), an essential structure in the cell walls of the vast majority of bacteria, is critical for division and maintaining cell shape and hydrostatic pressure. Bacteria comprising the Chlamydiales were thought to be one of the few exceptions. Chlamydia harbour genes for PG biosynthesis and exhibit susceptibility to 'anti-PG' antibiotics, yet attempts to detect PG in any chlamydial species have proven unsuccessful (the 'chlamydial anomaly'). We used a novel approach to metabolically label chlamydial PG using d-amino acid dipeptide probes and click chemistry. Replicating Chlamydia trachomatis were labelled with these probes throughout their biphasic developmental life cycle, and the results of differential probe incorporation experiments conducted in the presence of ampicillin are consistent with the presence of chlamydial PG-modifying enzymes. These findings culminate 50 years of speculation and debate concerning the chlamydial anomaly and are the strongest evidence so far that chlamydial species possess functional PG. [ABSTRACT FROM AUTHOR]

Splicing of precursor messenger RNA (pre-mRNA) in eukaryotic cells is carried out by the spliceosome, which consists of five small nuclear ribonucleoproteins (snRNPs) and a number of accessory factors and enzymes. Each snRNP contains a ring-shaped subcomplex of seven proteins and a specific RNA molecule. The U6 snRNP contains a unique heptameric Lsm protein complex, which specifically recognizes the U6 small nuclear RNA at its 3′ end. Here we report the crystal structures of the heptameric Lsm complex, both by itself and in complex with a 3′ fragment of U6 snRNA, at 2.8 Å resolution. Each of the seven Lsm proteins interacts with two neighbouring Lsm components to form a doughnut-shaped assembly, with the order Lsm3-2-8-4-7-5-6. The four uridine nucleotides at the 3′ end of U6 snRNA are modularly recognized by Lsm3, Lsm2, Lsm8 and Lsm4, with the uracil base specificity conferred by a highly conserved asparagine residue. The uracil base at the extreme 3′ end is sandwiched by His 36 and Arg 69 from Lsm3, through π-π and cation-π interactions, respectively. The distinctive end-recognition of U6 snRNA by the Lsm complex contrasts with RNA binding by the Sm complex in the other snRNPs. The structural features and associated biochemical analyses deepen mechanistic understanding of the U6 snRNP function in pre-mRNA splicing. [ABSTRACT FROM AUTHOR]

Strigolactones (SLs), a newly discovered class of carotenoid-derived phytohormones, are essential for developmental processes that shape plant architecture and interactions with parasitic weeds and symbiotic arbuscular mycorrhizal fungi. Despite the rapid progress in elucidating the SL biosynthetic pathway, the perception and signalling mechanisms of SL remain poorly understood. Here we show that DWARF 53 (D53) acts as a repressor of SL signalling and that SLs induce its degradation. We find that the rice (Oryza sativa) d53 mutant, which produces an exaggerated number of tillers compared to wild-type plants, is caused by a gain-of-function mutation and is insensitive to exogenous SL treatment. The D53 gene product shares predicted features with the class I Clp ATPase proteins and can form a complex with the α/β hydrolase protein DWARF 14 (D14) and the F-box protein DWARF 3 (D3), two previously identified signalling components potentially responsible for SL perception. We demonstrate that, in a D14- and D3-dependent manner, SLs induce D53 degradation by the proteasome and abrogate its activity in promoting axillary bud outgrowth. Our combined genetic and biochemical data reveal that D53 acts as a repressor of the SL signalling pathway, whose hormone-induced degradation represents a key molecular link between SL perception and responses. [ABSTRACT FROM AUTHOR]

An understanding of how quickly biomolecules bind and dissociate in cells is crucial for developing quantitative models of biology, but measurements of these kinetics were possible only using purified proteins in vitro — until now.A tool that opens up the development of quantitative models of biology. [ABSTRACT FROM AUTHOR]

Rupture of the plasma membrane in different forms of cell death was long thought to be a passive process. The finding that it is an active one, mediated by a specific membrane protein, reveals an unexpected feature shared by dying cells.NINJ1 protein mediates rupture of the plasma membrane in dying cells. [ABSTRACT FROM AUTHOR]

Crystallographer who defined rules of virus structure. [ABSTRACT FROM AUTHOR]

Despite the large size of the Xenopus laevis egg (approximately 1.2 mm diameter), a fertilized egg rapidly proceeds through mitosis in a spatially coordinated fashion. Mitosis is initiated by a bistable system of regulatory proteins centred on Cdk1 (refs 1, 2), raising the possibility that this spatial coordination could be achieved through trigger waves of Cdk1 activity. Using an extract system that performs cell cycles in vitro, here we show that mitosis does spread through Xenopus cytoplasm via trigger waves, propagating at a linear speed of approximately 60 µm min−1. Perturbing the feedback loops that give rise to the bistability of Cdk1 changes the speed and dynamics of the waves. Time-lapse imaging of intact eggs argues that trigger waves of Cdk1 activation are responsible for surface contraction waves, ripples in the cell cortex that precede cytokinesis. These findings indicate that Cdk1 trigger waves help ensure the spatiotemporal coordination of mitosis in large eggs. Trigger waves may be an important general mechanism for coordinating biochemical events over large distances. [ABSTRACT FROM AUTHOR]

Much of our current knowledge about mitochondria has come from studying patients who have respiratory chain disorders. These disorders comprise a large collection of individually rare syndromes, each presenting in a unique and often devastating way. In recent years, there has been great progress in defining their genetic basis, but we still know little about the cascade of events that gives rise to such diverse pathology. Here, we review these disorders and explore them in the context of a contemporary understanding of mitochondrial evolution, biochemistry and genetics. Fully deciphering their pathogenesis is a challenging next step that will inspire the development of drug treatments for rare and common diseases. [ABSTRACT FROM AUTHOR]

PIWI-family proteins and their associated small RNAs (piRNAs) act in an evolutionarily conserved innate immune mechanism to provide essential protection for germ-cell genomes against the activity of mobile genetic elements. piRNA populations comprise a molecular definition of transposons, which permits them to distinguish transposons from host genes and selectively silence them. piRNAs can be generated in two distinct ways, forming either primary or secondary piRNAs. Primary piRNAs come from discrete genomic loci, termed piRNA clusters, and seem to be derived from long, single-stranded precursors. The biogenesis of primary piRNAs involves at least two nucleolytic steps. An unknown enzyme cleaves piRNA cluster transcripts to generate monophosphorylated piRNA 5? ends. piRNA 3? ends are probably formed by exonucleolytic trimming, after a piRNA precursor is loaded into its PIWI partner. Secondary piRNAs arise during the adaptive 'ping-pong' cycle, with their 5? termini being formed by the activity of PIWIs themselves. A number of proteins have been implicated genetically in primary piRNA biogenesis. One of these, Drosophila melanogaster Zucchini, is a member of the phospholipase-D family of phosphodiesterases, which includes both phospholipases and nucleases. Here we produced a dimeric, soluble fragment of the mouse Zucchini homologue (mZuc; also known as PLD6) and show that it possesses single-strand-specific nuclease activity. A crystal structure of mZuc at 1.75?Å resolution indicates greater architectural similarity to phospholipase-D family nucleases than to phospholipases. Together, our data suggest that the Zucchini proteins act in primary piRNA biogenesis as nucleases, perhaps generating the 5? ends of primary piRNAs. [ABSTRACT FROM AUTHOR]

The article reports on the importance of structural biology, genomics and biochemistry on reinvigorating and old debate about the relationship between genes and disease. According to scientist Nicholas Katsanis, the molecular biological information gives them a much finer view of what really is clinically important. In connection, Katsanis and his team has published a paper on two diseases caused by malfunctioning cilia. The team has also did further studies in a zebrafish model and found that genes linked to the two conditions interact with each other during development.

An excerpt from the journal "Nature Chemical Biology" is presented.

Decoding post-transcriptional regulatory programs in RNA is a critical step towards the larger goal of developing predictive dynamical models of cellular behaviour. Despite recent efforts, the vast landscape of RNA regulatory elements remains largely uncharacterized. A long-standing obstacle is the contribution of local RNA secondary structure to the definition of interaction partners in a variety of regulatory contexts, including-but not limited to-transcript stability, alternative splicing and localization. There are many documented instances where the presence of a structural regulatory element dictates alternative splicing patterns (for example, human cardiac troponin T) or affects other aspects of RNA biology. Thus, a full characterization of post-transcriptional regulatory programs requires capturing information provided by both local secondary structures and the underlying sequence. Here we present a computational framework based on context-free grammars and mutual information that systematically explores the immense space of small structural elements and reveals motifs that are significantly informative of genome-wide measurements of RNA behaviour. By applying this framework to genome-wide human mRNA stability data, we reveal eight highly significant elements with substantial structural information, for the strongest of which we show a major role in global mRNA regulation. Through biochemistry, mass spectrometry and in vivo binding studies, we identified human HNRPA2B1 (heterogeneous nuclear ribonucleoprotein A2/B1, also known as HNRNPA2B1) as the key regulator that binds this element and stabilizes a large number of its target genes. We created a global post-transcriptional regulatory map based on the identity of the discovered linear and structural cis-regulatory elements, their regulatory interactions and their target pathways. This approach could also be used to reveal the structural elements that modulate other aspects of RNA behaviour. [ABSTRACT FROM AUTHOR]

Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyses the fixation of atmospheric CO2 in photosynthesis, but tends to form inactive complexes with its substrate ribulose 1,5-bisphosphate (RuBP). In plants, Rubisco is reactivated by the AAA+ (ATPases associated with various cellular activities) protein Rubisco activase (Rca), but no such protein is known for the Rubisco of red algae. Here we identify the protein CbbX as an activase of red-type Rubisco. The 3.0-Å crystal structure of unassembled CbbX from Rhodobacter sphaeroides revealed an AAA+ protein architecture. Electron microscopy and biochemical analysis showed that ATP and RuBP must bind to convert CbbX into functionally active, hexameric rings. The CbbX ATPase is strongly stimulated by RuBP and Rubisco. Mutational analysis suggests that CbbX functions by transiently pulling the carboxy-terminal peptide of the Rubisco large subunit into the hexamer pore, resulting in the release of the inhibitory RuBP. Understanding Rubisco activation may facilitate efforts to improve CO2 uptake and biomass production by photosynthetic organisms. [ABSTRACT FROM AUTHOR]

Two distinct microbial processes, denitrification and anaerobic ammonium oxidation (anammox), are responsible for the release of fixed nitrogen as dinitrogen gas (N2) to the atmosphere. Denitrification has been studied for over 100 years and its intermediates and enzymes are well known. Even though anammox is a key biogeochemical process of equal importance, its molecular mechanism is unknown, but it was proposed to proceed through hydrazine (N2H4). Here we show that N2H4 is produced from the anammox substrates ammonium and nitrite and that nitric oxide (NO) is the direct precursor of N2H4. We resolved the genes and proteins central to anammox metabolism and purified the key enzymes that catalyse N2H4 synthesis and its oxidation to N2. These results present a new biochemical reaction forging an N-N bond and fill a lacuna in our understanding of the biochemical synthesis of the N2 in the atmosphere. Furthermore, they reinforce the role of nitric oxide in the evolution of the nitrogen cycle. [ABSTRACT FROM AUTHOR]

Mature cortical pyramidal neurons receive excitatory inputs onto small protrusions emanating from their dendrites called spines. Spines undergo activity-dependent remodelling, stabilization and pruning during development, and similar structural changes can be triggered by learning and changes in sensory experiences. However, the biochemical triggers and mechanisms of de novo spine formation in the developing brain and the functional significance of new spines to neuronal connectivity are largely unknown. Here we develop an approach to induce and monitor de novo spine formation in real time using combined two-photon laser-scanning microscopy and two-photon laser uncaging of glutamate. Our data demonstrate that, in mouse cortical layer 2/3 pyramidal neurons, glutamate is sufficient to trigger de novo spine growth from the dendrite shaft in a location-specific manner. We find that glutamate-induced spinogenesis requires opening of NMDARs (N-methyl-d-aspartate-type glutamate receptors) and activation of protein kinase A (PKA) but is independent of calcium-calmodulin-dependent kinase II (CaMKII) and tyrosine kinase receptor B (TrkB) receptors. Furthermore, newly formed spines express glutamate receptors and are rapidly functional such that they transduce presynaptic activity into postsynaptic signals. Together, our data demonstrate that early neural connectivity is shaped by activity in a spatially precise manner and that nascent dendrite spines are rapidly functionally incorporated into cortical circuits. [ABSTRACT FROM AUTHOR]

A letter to the editor by Chris Kirk, is presented in response to the Editorial "What's in a name?," in the 2006 issue.

The article reports developments related to research in Portugal. There are 51 modular research laboratories in chemistry, biological chemistry, plant sciences and technology managed by the Institute for Chemical and Biological Technology. The average number of weekly visitors in 2006 to the "Nature" online from Portugal is 7,042.

Polycomb group (PcG) proteins are transcriptional repressors that control processes ranging from the maintenance of cell fate decisions and stem cell pluripotency in animals to the control of flowering time in plants. In Drosophila, genetic studies identified more than 15 different PcG proteins that are required to repress homeotic (HOX) and other developmental regulator genes in cells where they must stay inactive. Biochemical analyses established that these PcG proteins exist in distinct multiprotein complexes that bind to and modify chromatin of target genes. Among those, Polycomb repressive complex 1 (PRC1) and the related dRing-associated factors (dRAF) complex contain an E3 ligase activity for monoubiquitination of histone H2A (refs 1–4). Here we show that the uncharacterized Drosophila PcG gene calypso encodes the ubiquitin carboxy-terminal hydrolase BAP1. Biochemically purified Calypso exists in a complex with the PcG protein ASX, and this complex, named Polycomb repressive deubiquitinase (PR-DUB), is bound at PcG target genes in Drosophila. Reconstituted recombinant Drosophila and human PR-DUB complexes remove monoubiquitin from H2A but not from H2B in nucleosomes. Drosophila mutants lacking PR-DUB show a strong increase in the levels of monoubiquitinated H2A. A mutation that disrupts the catalytic activity of Calypso, or absence of the ASX subunit abolishes H2A deubiquitination in vitro and HOX gene repression in vivo. Polycomb gene silencing may thus entail a dynamic balance between H2A ubiquitination by PRC1 and dRAF, and H2A deubiquitination by PR-DUB. [ABSTRACT FROM AUTHOR]