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Natura 2000: EU Reserves Are Facing Development Pressures

Yale Environment 360 - Mon, 08/31/2015 - 07:23

An astonishing 18 percent of the European Union’s land area is protected under a network of preserves known as Natura 2000. Now, at the urging of business interests and farmers, the EU is examining whether regulations on development in these areas should be loosened. BY CHRISTIAN SCHWAGERL

Categories: Environmental News

NASA Study Quantifies Plants' Role in Mitigating Urban Heat Island Effect

Yale Environment 360 - Thu, 08/27/2015 - 09:56

The presence or scarcity of vegetation is an essential factor in determining how much urban areas heat up, according to a NASA study.

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Urban heat island effect Using data from multiple satellites, the researchers found that areas covered in part by impervious surfaces such as asphalt, concrete, and steel had an average summer temperature 3.4 degrees F higher than nearby rural areas. The highest U.S. urban temperatures compared to surrounding areas were along the Interstate-95 corridor from Boston to Washington and around Atlanta and the I-85 corridor in the Southeast. In desert cities such as Phoenix, the urban area was actually cooler because irrigated lawns and trees provide cooling that dry, rocky areas do not, the researchers explain. The urban heat island effect occurs primarily during the day, when impervious surfaces in cities absorb more sunlight than surrounding vegetated areas.

Categories: Environmental News

In Canadian Peaks, Scientists Track Impacts of Vanishing Ice

Yale Environment 360 - Thu, 08/27/2015 - 07:20



Earlier this month, a team of Canadian scientists braved a cold-weather thunderstorm, snow, rain, and high winds to spend a week working on the last extensive icefield in the interior of the Northwest Territories. Accompanying them was Yale Environment 360 contributor Ed Struzik, who reports on the trip and the importance of the research team’s investigations. The group worked on the Brintnell/Bologna icefield, which has shrunk by more than a third over the last three decades and continues to melt at a rapid clip. The scientists hope to determine how the melting of these glaciers and the loss of snowpack in the surrounding mountains might affect the region’s ecology and rivers, including the huge Mackenzie River, Canada’s largest.
Read more.

Categories: Environmental News

Lifetime collaborators reap the benefits

Nature - Thu, 08/27/2015 - 00:00

Lifetime collaborators reap the benefits

Nature 525, 7567 (2015). doi:10.1038/525009f

Author: Chris Woolston

Scientists with ‘super ties’ gain citation-rate reward.

Categories: Literature

Quantum ‘spookiness’ passes toughest test yet

Nature - Thu, 08/27/2015 - 00:00

Quantum ‘spookiness’ passes toughest test yet

Nature 525, 7567 (2015). http://www.nature.com/doifinder/10.1038/nature.2015.18255

Author: Zeeya Merali

Experiment plugs loopholes in previous demonstrations of 'action at a distance', against Einstein's objections — and could make data encryption safer.

Categories: Literature

U.S. Shale Gas Production Expected to Fall for First Time, Government Says

Yale Environment 360 - Wed, 08/26/2015 - 11:27

Natural gas production from all seven major shale formations in the U.S. is projected to drop next month for the first time since

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Monthly change in shale gas production the shale gas boom began in earnest roughly a decade ago, according to an analysis from the U.S. Energy Information Administration. Major shale regions produced gas at a record-high rate of 45.6 billion cubic feet per day in May, but that rate is expected to drop to 44.9 billion cubic feet per day in September, the report says. It attributes the decline to existing, legacy wells becoming significantly less productive and a substantial drop in the number of drilling rigs in each of the seven major shale regions since September 2014. New wells are being established, the EIA notes, but they are not producing enough natural gas to offset expected declines from legacy wells.

Categories: Environmental News

Next-generation X-ray source fires up

Nature - Wed, 08/26/2015 - 00:00

Next-generation X-ray source fires up

Nature 525, 7567 (2015). http://www.nature.com/doifinder/10.1038/nature.2015.18253

Author: Davide Castelvecchi

Swedish synchrotron promises to open up new avenues for researchers.

Categories: Literature

Neurodegeneration: Problems at the nuclear pore

Nature - Wed, 08/26/2015 - 00:00

Neurodegeneration: Problems at the nuclear pore

Nature 525, 7567 (2015). doi:10.1038/nature15208

Authors: Bennett W. Fox & Randal S. Tibbetts

Expansion of a repetitive DNA sequence is associated with neurodegeneration. Three studies identify genes involved in nuclear import and export that can mediate the toxicity this expansion causes. See Article p.56 & Letter p.129

Categories: Literature

Molecular biology: Unequal opportunity during class switching

Nature - Wed, 08/26/2015 - 00:00

Molecular biology: Unequal opportunity during class switching

Nature 525, 7567 (2015). doi:10.1038/nature15209

Authors: Javier M. Di Noia

The DNA breakage-and-repair mechanism that generates antibodies of different classes has, in theory, a 50% chance of occurring correctly. But this recombination turns out to be heavily biased towards productive events. See Letter p.134

Categories: Literature

The C9orf72 repeat expansion disrupts nucleocytoplasmic transport

Nature - Wed, 08/26/2015 - 00:00

The C9orf72 repeat expansion disrupts nucleocytoplasmic transport

Nature 525, 7567 (2015). doi:10.1038/nature14973

Authors: Ke Zhang, Christopher J. Donnelly, Aaron R. Haeusler, Jonathan C. Grima, James B. Machamer, Peter Steinwald, Elizabeth L. Daley, Sean J. Miller, Kathleen M. Cunningham, Svetlana Vidensky, Saksham Gupta, Michael A. Thomas, Ingie Hong, Shu-Ling Chiu, Richard L. Huganir, Lyle W. Ostrow, Michael J. Matunis, Jiou Wang, Rita Sattler, Thomas E. Lloyd & Jeffrey D. Rothstein

The hexanucleotide repeat expansion (HRE) GGGGCC (G4C2) in C9orf72 is the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Recent studies support an HRE RNA gain-of-function mechanism of neurotoxicity, and we previously identified protein interactors for

Categories: Literature

Alcohols as alkylating agents in heteroarene C–H functionalization

Nature - Wed, 08/26/2015 - 00:00

Alcohols as alkylating agents in heteroarene C–H functionalization

Nature 525, 7567 (2015). doi:10.1038/nature14885

Authors: Jian Jin & David W. C. MacMillan

Redox processes and radical intermediates are found in many biochemical processes, including deoxyribonucleotide synthesis and oxidative DNA damage. One of the core principles underlying DNA biosynthesis is the radical-mediated elimination of H2O to deoxygenate ribonucleotides, an example of ‘spin-centre shift’, during which an alcohol C–O bond is cleaved, resulting in a carbon-centred radical intermediate. Although spin-centre shift is a well-understood biochemical process, it is underused by the synthetic organic chemistry community. We wondered whether it would be possible to take advantage of this naturally occurring process to accomplish mild, non-traditional alkylation reactions using alcohols as radical precursors. Because conventional radical-based alkylation methods require the use of stoichiometric oxidants, increased temperatures or peroxides, a mild protocol using simple and abundant alkylating agents would have considerable use in the synthesis of diversely functionalized pharmacophores. Here we describe the development of a dual catalytic alkylation of heteroarenes, using alcohols as mild alkylating reagents. This method represents the first, to our knowledge, broadly applicable use of unactivated alcohols as latent alkylating reagents, achieved via the successful merger of photoredox and hydrogen atom transfer catalysis. The value of this multi-catalytic protocol has been demonstrated through the late-stage functionalization of the medicinal agents, fasudil and milrinone.

Categories: Literature

GGGGCC repeat expansion in C9orf72 compromises nucleocytoplasmic transport

Nature - Wed, 08/26/2015 - 00:00

GGGGCC repeat expansion in C9orf72 compromises nucleocytoplasmic transport

Nature 525, 7567 (2015). doi:10.1038/nature14974

Authors: Brian D. Freibaum, Yubing Lu, Rodrigo Lopez-Gonzalez, Nam Chul Kim, Sandra Almeida, Kyung-Ha Lee, Nisha Badders, Marc Valentine, Bruce L. Miller, Philip C. Wong, Leonard Petrucelli, Hong Joo Kim, Fen-Biao Gao & J. Paul Taylor

The GGGGCC (G4C2) repeat expansion in a noncoding region of C9orf72 is the most common cause of sporadic and familial forms of amyotrophic lateral sclerosis and frontotemporal dementia. The basis for pathogenesis is unknown. To elucidate the consequences of G4C2 repeat expansion in a tractable genetic system, we generated transgenic fly lines expressing 8, 28 or 58 G4C2-repeat-containing transcripts that do not have a translation start site (AUG) but contain an open-reading frame for green fluorescent protein to detect repeat-associated non-AUG (RAN) translation. We show that these transgenic animals display dosage-dependent, repeat-length-dependent degeneration in neuronal tissues and RAN translation of dipeptide repeat (DPR) proteins, as observed in patients with C9orf72-related disease. This model was used in a large-scale, unbiased genetic screen, ultimately leading to the identification of 18 genetic modifiers that encode components of the nuclear pore complex (NPC), as well as the machinery that coordinates the export of nuclear RNA and the import of nuclear proteins. Consistent with these results, we found morphological abnormalities in the architecture of the nuclear envelope in cells expressing expanded G4C2 repeats in vitro and in vivo. Moreover, we identified a substantial defect in RNA export resulting in retention of RNA in the nuclei of Drosophila cells expressing expanded G4C2 repeats and also in mammalian cells, including aged induced pluripotent stem-cell-derived neurons from patients with C9orf72-related disease. These studies show that a primary consequence of G4C2 repeat expansion is the compromise of nucleocytoplasmic transport through the nuclear pore, revealing a novel mechanism of neurodegeneration.

Categories: Literature

Orientation-specific joining of AID-initiated DNA breaks promotes antibody class switching

Nature - Wed, 08/26/2015 - 00:00

Orientation-specific joining of AID-initiated DNA breaks promotes antibody class switching

Nature 525, 7567 (2015). doi:10.1038/nature14970

Authors: Junchao Dong, Rohit A. Panchakshari, Tingting Zhang, Yu Zhang, Jiazhi Hu, Sabrina A. Volpi, Robin M. Meyers, Yu-Jui Ho, Zhou Du, Davide F. Robbiani, Feilong Meng, Monica Gostissa, Michel C. Nussenzweig, John P. Manis & Frederick W. Alt

During B-cell development, RAG endonuclease cleaves immunoglobulin heavy chain (IgH) V, D, and J gene segments and orchestrates their fusion as deletional events that assemble a V(D)J exon in the same transcriptional orientation as adjacent Cμ constant region exons. In mice, six additional sets of constant region exons (CHs) lie 100–200 kilobases downstream in the same transcriptional orientation as V(D)J and Cμ exons. Long repetitive switch (S) regions precede Cμ and downstream CHs. In mature B cells, class switch recombination (CSR) generates different antibody classes by replacing Cμ with a downstream CH (ref. 2). Activation-induced cytidine deaminase (AID) initiates CSR by promoting deamination lesions within Sμ and a downstream acceptor S region; these lesions are converted into DNA double-strand breaks (DSBs) by general DNA repair factors. Productive CSR must occur in a deletional orientation by joining the upstream end of an Sμ DSB to the downstream end of an acceptor S-region DSB. However, the relative frequency of deletional to inversional CSR junctions has not been measured. Thus, whether orientation-specific joining is a programmed mechanistic feature of CSR as it is for V(D)J recombination and, if so, how this is achieved is unknown. To address this question, we adapt high-throughput genome-wide translocation sequencing into a highly sensitive DSB end-joining assay and apply it to endogenous AID-initiated S-region DSBs in mouse B cells. We show that CSR is programmed to occur in a productive deletional orientation and does so via an unprecedented mechanism that involves in cis Igh organizational features in combination with frequent S-region DSBs initiated by AID. We further implicate ATM-dependent DSB-response factors in enforcing this mechanism and provide an explanation of why CSR is so reliant on the 53BP1 DSB-response factor.

Categories: Literature

A four-helix bundle stores copper for methane oxidation

Nature - Wed, 08/26/2015 - 00:00

A four-helix bundle stores copper for methane oxidation

Nature 525, 7567 (2015). doi:10.1038/nature14854

Authors: Nicolas Vita, Semeli Platsaki, Arnaud Baslé, Stephen J. Allen, Neil G. Paterson, Andrew T. Crombie, J. Colin Murrell, Kevin J. Waldron & Christopher Dennison

Methane-oxidizing bacteria (methanotrophs) require large quantities of copper for the membrane-bound (particulate) methane monooxygenase. Certain methanotrophs are also able to switch to using the iron-containing soluble methane monooxygenase to catalyse methane oxidation, with this switchover regulated by copper. Methane monooxygenases are nature’s primary biological mechanism for suppressing atmospheric levels of methane, a potent greenhouse gas. Furthermore, methanotrophs and methane monooxygenases have enormous potential in bioremediation and for biotransformations producing bulk and fine chemicals, and in bioenergy, particularly considering increased methane availability from renewable sources and hydraulic fracturing of shale rock. Here we discover and characterize a novel copper storage protein (Csp1) from the methanotroph Methylosinus trichosporium OB3b that is exported from the cytosol, and stores copper for particulate methane monooxygenase. Csp1 is a tetramer of four-helix bundles with each monomer binding up to 13 Cu(I) ions in a previously unseen manner via mainly Cys residues that point into the core of the bundle. Csp1 is the first example of a protein that stores a metal within an established protein-folding motif. This work provides a detailed insight into how methanotrophs accumulate copper for the oxidation of methane. Understanding this process is essential if the wide-ranging biotechnological applications of methanotrophs are to be realized. Cytosolic homologues of Csp1 are present in diverse bacteria, thus challenging the dogma that such organisms do not use copper in this location.

Categories: Literature

FDA vulnerability revealed

Nature - Wed, 08/26/2015 - 00:00

FDA vulnerability revealed

Nature 524, 7566 (2015). doi:10.1038/524387a

A politically charged advisory committee meeting may have tipped the scales in favour of a mildly effective female libido drug.

Categories: Literature

We must build resilience into our communities

Nature - Wed, 08/26/2015 - 00:00

We must build resilience into our communities

Nature 524, 7566 (2015). http://www.nature.com/doifinder/10.1038/524389a

Author: Erwann Michel-Kerjan

Innovative approaches can better equip society to deal with natural disasters and other shocks, says Erwann Michel-Kerjan.

Categories: Literature

Animal behaviour: Hummingbirds sip using mini pumps

Nature - Wed, 08/26/2015 - 00:00

Animal behaviour: Hummingbirds sip using mini pumps

Nature 524, 7566 (2015). doi:10.1038/524390a

Hummingbirds draw nectar into their bills using long tongues that act like tiny pumps.It was long thought that liquid travels passively up the birds' tongues without suction. But Alejandro Rico-Guevara and his colleagues at the University of Connecticut in Storrs found a different mechanism

Categories: Literature

Chemistry: Better catalyst for carbon conversion

Nature - Wed, 08/26/2015 - 00:00

Chemistry: Better catalyst for carbon conversion

Nature 524, 7566 (2015). doi:10.1038/524390b

A porous, crystalline compound can speed up the conversion of carbon dioxide to carbon monoxide in water.Omar Yaghi and Christopher Chang at the University of California, Berkeley, and their colleagues used structures called covalent organic frameworks (COFs) — grid-like arrangements of carbon, nitrogen and

Categories: Literature

Animal behaviour: Stinging cells help jellyfish to mate

Nature - Wed, 08/26/2015 - 00:00

Animal behaviour: Stinging cells help jellyfish to mate

Nature 524, 7566 (2015). doi:10.1038/524390c

Some box jellyfish display elaborate mating behaviours and even use their toxic stinging cells to ensure successful fertilization.Many jellyfish reproduce using external fertilization, but in a few box jellyfish, fertilization can occur internally. In one species (Copula sivickisi; pictured), the male

Categories: Literature

Astrophysics: Dark-energy search narrows

Nature - Wed, 08/26/2015 - 00:00

Astrophysics: Dark-energy search narrows

Nature 524, 7566 (2015). doi:10.1038/524390d

Two groups have tightened the limits on the search for elusive dark matter and dark energy, the mysterious force accelerating the expansion of the Universe.Physicists have proposed that dark energy could come from a 'chameleon' field: a force that would act in the low

Categories: Literature

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