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Learning regulatory programs by threshold SVD [Statistics]

PNAS Early Edition Articles - Mon, 10/20/2014 - 13:02
We formulate a statistical model for the regulation of global gene expression by multiple regulatory programs and propose a thresholding singular value decomposition (T-SVD) regression method for learning such a model from data. Extensive simulations demonstrate that this method offers improved computational speed and higher sensitivity and specificity over competing...

Adiponectin, physical exercise, and neurogenesis [Neuroscience]

PNAS Early Edition Articles - Mon, 10/20/2014 - 13:02
Adiponectin (ADN) is an adipocyte-secreted protein with insulin-sensitizing, antidiabetic, antiinflammatory, and antiatherogenic properties. Evidence is also accumulating that ADN has neuroprotective activities, yet the underlying mechanism remains elusive. Here we show that ADN could pass through the blood–brain barrier, and elevating its levels in the brain increased cell proliferation and...

Drosophila TDP1 [Neuroscience]

PNAS Early Edition Articles - Mon, 10/20/2014 - 13:02
Tyrosyl-DNA phosphodiesterase (TDP1) is a phylogenetically conserved enzyme critical for the removal of blocking lesions at the 3′ ends of DNA or RNA. This study analyzes the Drosophila TDP1 gene ortholog glaikit (gkt) and its possible role(s) in the repair of endogenous DNA lesions and neuroprotection. To do so, we...

Motive attribution asymmetry [Psychological and Cognitive Sciences]

PNAS Early Edition Articles - Mon, 10/20/2014 - 13:02
Five studies across cultures involving 661 American Democrats and Republicans, 995 Israelis, and 1,266 Palestinians provide previously unidentified evidence of a fundamental bias, what we term the “motive attribution asymmetry,” driving seemingly intractable human conflict. These studies show that in political and ethnoreligious intergroup conflict, adversaries tend to attribute their...

Rescue of dopamine by NSCs in PD rats [Neuroscience]

PNAS Early Edition Articles - Mon, 10/20/2014 - 13:02
Embryonic stem cell-based therapies exhibit great potential for the treatment of Parkinson’s disease (PD) because they can significantly rescue PD-like behaviors. However, whether the transplanted cells themselves release dopamine in vivo remains elusive. We and others have recently induced human embryonic stem cells into primitive neural stem cells (pNSCs) that...

OsABCC1 reduces As accumulation in rice grain [Agricultural Sciences]

PNAS Early Edition Articles - Mon, 10/20/2014 - 13:02
Arsenic (As) is a chronic poison that causes severe skin lesions and cancer. Rice (Oryza sativa L.) is a major dietary source of As; therefore, reducing As accumulation in the rice grain and thereby diminishing the amount of As that enters the food chain is of critical importance. Here, we...

Direct numerical simulations of wind ripples [Earth, Atmospheric, and Planetary Sciences]

PNAS Early Edition Articles - Mon, 10/20/2014 - 13:02
Aeolian sand beds exhibit regular patterns of ripples resulting from the interaction between topography and sediment transport. Their characteristics have been so far related to reptation transport caused by the impacts on the ground of grains entrained by the wind into saltation. By means of direct numerical simulations of grains...

Fe atom catalysis and diffusion at graphene edges [Chemistry]

PNAS Early Edition Articles - Mon, 10/20/2014 - 13:02
Single-atom catalysts are of great interest because of their high efficiency. In the case of chemically deposited sp2 carbon, the implementation of a single transition metal atom for growth can provide crucial insight into the formation mechanisms of graphene and carbon nanotubes. This knowledge is particularly important if we are...

Fam20B activates proteoglycan synthesis [Biochemistry]

PNAS Early Edition Articles - Mon, 10/20/2014 - 13:02
Most eukaryotic cells elaborate several proteoglycans critical for transmitting biochemical signals into and between cells. However, the regulation of proteoglycan biosynthesis is not completely understood. We show that the atypical secretory kinase family with sequence similarity 20, member B (Fam20B) phosphorylates the initiating xylose residue in the proteoglycan tetrasaccharide linkage...

NMR of Ran complexed with Mengo Leader protein [Microbiology]

PNAS Early Edition Articles - Mon, 10/20/2014 - 13:02
Cardiovirus Leader (L) proteins induce potent antihost inhibition of active cellular nucleocytoplasmic trafficking by triggering aberrant hyperphosphorylation of nuclear pore proteins (Nup). To achieve this, L binds protein RanGTPase (Ran), a key trafficking regulator, and diverts it into tertiary or quaternary complexes with required kinases. The activity of L is...

El Nino Southern Oscillation and global flood risk [Environmental Sciences]

PNAS Early Edition Articles - Mon, 10/20/2014 - 13:02
El Niño Southern Oscillation (ENSO) is the most dominant interannual signal of climate variability and has a strong influence on climate over large parts of the world. In turn, it strongly influences many natural hazards (such as hurricanes and droughts) and their resulting socioeconomic impacts, including economic damage and loss...

Disease-associated tolerance in transmitters [Immunology and Inflammation]

PNAS Early Edition Articles - Mon, 10/20/2014 - 13:02
Natural populations show striking heterogeneity in their ability to transmit disease. For example, a minority of infected individuals known as superspreaders carries out the majority of pathogen transmission events. In a mouse model of Salmonella infection, a subset of infected hosts becomes superspreaders, shedding high levels of bacteria (>108 cfu...

Engineering epoxide hydrolase for bulky substrates [Applied Biological Sciences]

PNAS Early Edition Articles - Mon, 10/20/2014 - 13:02
Optically pure epoxides are essential chiral precursors for the production of (S)-propranolol, (S)-alprenolol, and other β-adrenergic receptor blocking drugs. Although the enzymatic production of these bulky epoxides has proven difficult, here we report a method to effectively improve the activity of BmEH, an epoxide hydrolase from Bacillus megaterium ECU1001 toward...

Anosteocytic bone remodeling challenges paradigms [Evolution]

PNAS Early Edition Articles - Mon, 10/20/2014 - 13:02
A remarkable property of tetrapod bone is its ability to detect and remodel areas where damage has accumulated through prolonged use. This process, believed vital to the long-term health of bone, is considered to be initiated and orchestrated by osteocytes, cells within the bone matrix. It is therefore surprising that...

Ultra-high-resolution lipid biomarker stratigraphy [Earth, Atmospheric, and Planetary Sciences]

PNAS Early Edition Articles - Mon, 10/20/2014 - 13:02
Marine microorganisms adapt to their habitat by structural modification of their membrane lipids. This concept is the basis of numerous molecular proxies used for paleoenvironmental reconstruction. Archaeal tetraether lipids from ubiquitous marine planktonic archaea are particularly abundant, well preserved in the sedimentary record and used in several molecular proxies. We...

CpGV resistance in codling moth depends on viral pe38 [Applied Biological Sciences]

PNAS Early Edition Articles - Mon, 10/20/2014 - 13:02
The baculovirus Cydia pomonella granulovirus (CpGV) is widely applied as a biocontrol agent of codling moth. After field resistance of codling moth populations had been observed against the commercially used Mexican (M) isolate of CpGV, infection experiments of larvae of the resistant codling moth strain CpRR1 showed that several other...

Flagellar motor switching dynamics [Biophysics and Computational Biology]

PNAS Early Edition Articles - Mon, 10/20/2014 - 13:02
Switching dynamics of flagellar motors of Escherichia coli is commonly observed through markers attached to the flagellar filaments. To eliminate possible complications resulting from the conformational transitions of these filaments and to look at the output of motors more directly, we monitored motor rotation by attaching nanogold spheres to the...

Tarantula toxins probe ion channel activity [Physiology]

PNAS Early Edition Articles - Mon, 10/20/2014 - 13:02
Electrically excitable cells, such as neurons, exhibit tremendous diversity in their firing patterns, a consequence of the complex collection of ion channels present in any specific cell. Although numerous methods are capable of measuring cellular electrical signals, understanding which types of ion channels give rise to these signals remains a...
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