Sometimes there’s just no telling what will turn up at the local market. Fish biologist Jeff Williams of the Smithsonian’s National Museum of Natural History […]

The post Surprise: Distinctive new surgeonfish species makes an improbable debut appeared first on Smithsonian Insider.

For more than 60 years, researchers have tried to successfully cryopreserve (or freeze) the embryo of zebrafish, a species that is an important medical model […]

The post Gold nanotechnology and lasers used to successfully freeze fish embryos appeared first on Smithsonian Insider.

In a new study in which one of humankind’s most high-tech tools was used to analyze one of its most primitive, scientists have uncovered evidence […]

The post Laser beams unveil secrets locked inside primitive stone spear points appeared first on Smithsonian Insider.

The next time you swat a fly ponder this: inside its belly is the DNA of whatever it ate before landing on your picnic dinner—roadkill, […]

The post Innovation: Belly gunk from flies used to survey forest animals appeared first on Smithsonian Insider.

In everyday life, ultraviolet, or UV, light earns a bad reputation for being responsible for sunburns and other harmful effects on humans. However, research suggests […]

The post In search for life, ultraviolet light may be ultra important appeared first on Smithsonian Insider.

Hundreds of experiments have shown biodiversity fosters healthier, more productive ecosystems. But many experts doubted whether these experiments would hold up in the real world. […]

The post In the wild, biodiversity’s power surpasses what experiments predict appeared first on Smithsonian Insider.

When fast radio bursts, or FRBs, were first detected in 2001, astronomers had never seen anything like them before. Since then, astronomers have found a […]

The post New study indicates mysterious fast radio bursts occur in universe every second appeared first on Smithsonian Insider.

Three former scientists from the Smithsonian’s National Zoological Park–Ellen Lamirande, Don Nichols, and Allan Pessier–were honored at the sixth annual Golden Goose Award ceremony at […]

The post Zoo scientists honored at Golden Goose appeared first on Smithsonian Insider.

Chances are, if you’ve been stung by a jellyfish along the Chesapeake Bay it was by a sea nettle jellyfish–one of the most common and […]

The post Scientists discover common sea nettle jellyfish is actually two distinct species appeared first on Smithsonian Insider.

This animation shows how binary neutron stars warp space-time to create gravitational waves, then collide and explode into a visible kilonova, which can be detected […]

The post Astronomers see light show associated with gravitational waves appeared first on Smithsonian Insider.

According to a new survey of residents living near two major national parks in Panama, jaguars deserve increased protection. Nature and wildlife are considered national […]

The post Jaguar conservation depends on neighbor attitudes appeared first on Smithsonian Insider.

In 1854, a curious-looking spider was found preserved in 50 million-year-old amber. With an elongated neck-like structure and long mouthparts that protruded from the “head” […]

The post These newly discovered pelican spiders will make you want to visit Madagascar appeared first on Smithsonian Insider.

Every day, astronomers at the Harvard-Smithsonian Center for Astrophysics depend on computers to help them solve the mysteries of the universe, just as they did […]

The post Underpaid women “computers” mapped the universe in the 19th century appeared first on Smithsonian Insider.

This winter has brought many intense and powerful storms, with cold fronts sweeping across much of the United States. On a much grander scale, astronomers […]

The post Scientists surprised by relentless cosmic cold front appeared first on Smithsonian Insider.

When “2001: A Space Odyssey” premiered April 2, 1968 at Washington, D.C.’s Uptown Theater—not far from the Smithsonian’s National Air and Space Museum—not everyone was […]

The post The real history behind science fiction’s ‘2001: A Space Odyssey’ appeared first on Smithsonian Insider.

People often use the words turtle and tortoise interchangeably, but these reptiles have distinct differences: Turtle shells are typically more flattened and not as deeply […]

The post Five fun turtle and tortoise facts from the Smithsonian’s National Zoo appeared first on Smithsonian Insider.

In the early 20th century, Canada geese were considered endangered in the U.S. So in the 1950s and 1960s, birds from the Midwest were released […]

The post Study of bacteria inside guts of wild Canada geese shows greater danger than earlier studies exposed appeared first on Smithsonian Insider.

Ninety Limosa harlequin frogs (Atelopus limosus) bred in human care are braving the elements of the wild after Smithsonian scientists sent them out into the […]

The post Panama: First release of endangered frogs appeared first on Smithsonian Insider.

Five new species of snail-eating snake, from a group of snakes affectionately known to scientists as “goo-eaters,” have been discovered by a team working in […]

The post Newly discovered snakes use curved teeth to pry snails from their shells appeared first on Smithsonian Insider.

l-Hydroxyproline (l-Hyp) is a nonstandard amino acid that is present in certain proteins, in some antibiotics and in the cell-wall components of plants. l-Hyp is the product of the post-translational modification of protein prolines by prolyl hydroxylase enzymes, and the isomers trans-3-hydroxy-l-proline (T3LHyp) and trans-4-hydroxy-l-proline (T4LHyp) are major components of mammalian collagen. T4LHyp follows two distinct degradation pathways in bacteria and mammals, while T3LHyp is metabolized by a two-step metabolic pathway that is conserved in bacteria and mammals, which involves a T3LHyp dehydratase and a Δ1-pyrroline-2-carboxylate (Pyr2C) reductase. In order to shed light on the structure and catalysis of the enzyme involved in the second step of the T3LHyp degradation pathway, the crystal structure of Pyr2C reductase from the archaeon Thermococcus litoralis DSM 5473 complexed with NADH and l-proline is presented. The model allows the mapping of the residues involved in cofactor and product binding and represents a valid model for rationalizing the catalysis of Pyr2C reductases.

Aldo-keto reductases (AKRs) are NADPH/NADP+-dependent oxidoreductase enzymes that metabolize an aldehyde/ketone to the corresponding alcohol. AKR4C14 from rice exhibits a much higher efficiency in metabolizing malondialdehyde (MDA) than do the Arabidopsis enzymes AKR4C8 and AKR4C9, despite sharing greater than 60% amino-acid sequence identity. This study confirms the role of rice AKR4C14 in the detoxification of methylglyoxal and MDA, and demonstrates that the endogenous contents of both aldehydes in transgenic Arabidopsis ectopically expressing AKR4C14 are significantly lower than their levels in the wild type. The apo structure of indica rice AKR4C14 was also determined in the absence of the cofactor, revealing the stabilized open conformation. This is the first crystal structure in AKR subfamily 4C from rice to be observed in the apo form (without bound NADP+). The refined AKR4C14 structure reveals a stabilized open conformation of loop B, suggesting the initial phase prior to cofactor binding. Based on the X-ray crystal structure, the substrate- and cofactor-binding pockets of AKR4C14 are formed by loops A, B, C and β1α1. Moreover, the residues Ser211 and Asn220 on loop B are proposed as the hinge residues that are responsible for conformational alteration while the cofactor binds. The open conformation of loop B is proposed to involve Phe216 pointing out from the cofactor-binding site and the opening of the safety belt. Structural comparison with other AKRs in subfamily 4C emphasizes the role of the substrate-channel wall, consisting of Trp24, Trp115, Tyr206, Phe216, Leu291 and Phe295, in substrate discrimination. In particular, Leu291 could contribute greatly to substrate selectivity, explaining the preference of AKR4C14 for its straight-chain aldehyde substrate.

Pullulanase (EC 3.2.1.41) is a well known starch-debranching enzyme that catalyzes the cleavage of α-1,6-glycosidic linkages in α-glucans such as starch and pullulan. Crystal structures of a type I pullulanase from Paenibacillus barengoltzii (PbPulA) and of PbPulA in complex with maltopentaose (G5), maltohexaose (G6)/α-cyclodextrin (α-CD) and β-cyclodextrin (β-CD) were determined in order to better understand substrate binding to this enzyme. PbPulA belongs to glycoside hydrolase (GH) family 13 subfamily 14 and is composed of three domains (CBM48, A and C). Three carbohydrate-binding sites identified in PbPulA were located in CBM48, near the active site and in domain C, respectively. The binding site in CBM48 was specific for β-CD, while that in domain C has not been reported for other pullulanases. The domain C binding site had higher affinity for α-CD than for G6; a small motif (FGGEH) seemed to be one of the major determinants for carbohydrate binding in this domain. Structure-based mutations of several surface-exposed aromatic residues in CBM48 and domain C had a debilitating effect on the activity of the enzyme. These results suggest that both CBM48 and domain C play a role in binding substrates. The crystal forms described contribute to the understanding of pullulanase domain–carbohydrate interactions.

Death-associated protein kinase 1 (DAPK1) is a serine/threonine protein kinase that regulates apoptosis and autophagy. DAPK1 is considered to be a therapeutic target for amyloid-β deposition, endometrial adenocarcinomas and acute ischemic stroke. Here, the potent inhibitory activity of the natural anthraquinone purpurin against DAPK1 phosphorylation is shown. Thermodynamic analysis revealed that while the binding affinity of purpurin is similar to that of CPR005231, which is a DAPK1 inhibitor with an imidazopyridazine moiety, the binding of purpurin was more enthalpically favorable. In addition, the inhibition potencies were correlated with the enthalpic changes but not with the binding affinities. Crystallographic analysis of the DAPK1–purpurin complex revealed that the formation of a hydrogen-bond network is likely to contribute to the favorable enthalpic changes and that stabilization of the glycine-rich loop may cause less favorable entropic changes. The present findings indicate that purpurin may be a good lead compound for the discovery of inhibitors of DAPK1, and the observation of enthalpic changes could provide important clues for drug development.

The bond-valence method has been used for valence calculations of FeMo/V cofactors in FeMo/V proteins using 51 crystallographic data sets of FeMo/V proteins from the Protein Data Bank. The calculations show molybdenum(III) to be present in MoFe7S9C(Cys)(HHis)[R-(H)homocit] (where H4homocit is homocitric acid, HCys is cysteine and HHis is histidine) in FeMo cofactors, while vanadium(III) with a more reduced iron complement is obtained for FeV cofactors. Using an error analysis of the calculated valences, it was found that in FeMo cofactors Fe1, Fe6 and Fe7 can be unambiguously assigned as iron(III), while Fe2, Fe3, Fe4 and Fe5 show different degrees of mixed valences for the individual Fe atoms. For the FeV cofactors in PDB entry 5n6y, Fe4, Fe5 and Fe6 correspond to iron(II), iron(II) and iron(III), respectively, while Fe1, Fe2, Fe3 and Fe7 exhibit strongly mixed valences. Special situations such as CO-bound and selenium-substituted FeMo cofactors and O(N)H-bridged FeV cofactors are also discussed and suggest rearrangement of the electron configuration on the substitution of the bridging S atoms.

Despite the importance of seasonally dry forests, little is known of their ecology. Now, a new book The Ecology and Conservation of Seasonally Dry Forests in Asia, published by Smithsonian Institution Scholarly Press, explores these unique ecosystems, its animals, plants, and the people that inhabit them.

The post New book: The Ecology and Conservation of Seasonally Dry Forests in Asia appeared first on Smithsonian Insider.

Warner’s narrative covers the major natural sweeteners, including sugar, molasses from cane, beet sugar, corn syrup, honey and maple, as well as artificial sweeteners such as saccharin, cyclamate, aspartame and sucralose.

The post New Book: “Sweet Stuff: An American History of Sweeteners from Sugar to Sucralose” appeared first on Smithsonian Insider.

Now, for the first time, Charles Darwin's life is portrayed pictorially in an illustrated biography in graphic novel-style for all ages to enjoy.

The post “Darwin: A Graphic Biography,” new release from Smithsonian Books appeared first on Smithsonian Insider.

This Secret Smithsonian Adventures series follows four middle schoolers as they foil events by two dastardly doers who try to dangerously change the true course […]

The post Secret Adventures: “Claws and Effect” appeared first on Smithsonian Insider.

For the first time in its history the Smithsonian’s National Museum of African Art opened an exhibition on the continent of Africa. “Chief S.O. Alonge: […]

The post A first: Smithsonian’s African Art Museum opens exhibition in Africa appeared first on Smithsonian Insider.

Yinlong Song, Yikan Zhang, Ying Pan, Jianfeng He, Yan Wang, Wei Chen, Jing Guo, Haiteng Deng, Yi Xue, Xianyang Fang, and Xin Liang

Microtubules dynamics is regulated by the plus end-tracking proteins (+TIPs) in cells. End binding protein 1 (EB1) acts as a master regulator in +TIPs networks by targeting microtubule growing ends and recruiting other factors. However, the molecular mechanism of how EB1 binds to microtubule ends with a high affinity remains to be an open question. Using single-molecule imaging, we show that the end-binding kinetics of EB1 changes along with the polymerizing and hydrolysis rate of tubulin dimers, confirming the binding of EB1 to GTP/GDP-Pi tubulin at microtubule growing ends. The affinity of wild-type EB1 to these sites is higher than monomeric EB1 mutants, suggesting that two CH domains in the dimer contribute to the end-binding. Introducing phosphomimicking mutations into the linker domain of EB1 weakens the end-binding affinity and confers a more curved conformation to EB1 dimer without compromising dimerization, suggesting that the overall architecture of EB1 is important for the end-binding affinity. Taken together, our results provide insights into understanding how the high-affinity end-binding of EB1 can be achieved and how this activity may be regulated in cells.

Imke K. Mandemaker, Di Zhou, Serena T. Bruens, Dick H. Dekkers, Pernette J. Verschure, Raghu R. Edupuganti, Eran Meshorer, Jeroen A. Demmers, and Jurgen A. Marteijn

Many chromatin remodeling and modifying proteins are involved in the DNA damage response by stimulating repair or inducing DNA damage signaling. Interestingly, here we identified that down regulation of the H1-interacting protein SET results in increased resistance to a wide variety of DNA damaging agents. We found that this increased resistance is not the result of an inhibitory effect of SET on DNA repair, but rather the consequence of a suppressed apoptotic response to DNA damage. We further provide evidence that the histone chaperone SET is responsible for the eviction of H1 from chromatin. Knock down of H1 in SET-depleted cells resulted in re-sensitization of cells to DNA damage, suggesting that the increased DNA damage resistance in SET-depleted cells is the result of enhanced retention of H1 on chromatin. Finally, clonogenic survival assays show that SET and p53 are epistatic in attenuating DNA damage-induced cell death. Altogether, our data show a role for SET in the DNA damage response as a regulator of cell survival following genotoxic stress.

Scott J. Neal, Qingxiang Zhou, and Francesca Pignoni

The specification of organs, tissues and cell types results from cell fate restrictions enacted by nuclear transcription factors under the control of conserved signaling pathways. The progenitor epithelium of the Drosophila compound eye, the eye imaginal disc, is a premier model for the study of such processes. Early in development, apposing cells of the eye disc are established as either retinal progenitors or support cells of the peripodial epithelium (PE), in a process whose genetic and mechanistic determinants are poorly understood. We have identified Protein Phosphatase 2A (PP2A), and specifically a STRIPAK-PP2A complex that includes the scaffolding and substrate-specificity components Cka, Strip and SLMAP, as a critical player in the retina-PE fate choice. We show that these factors suppress ectopic retina formation in the presumptive PE and do so via the Hippo signaling axis. STRIPAK-PP2A negatively regulates Hpo kinase, and consequently its substrate Wts, to release the transcriptional co-activator Yki into the nucleus. Thus, a modular higher-order PP2A complex refines the activity of this general phosphatase to act in a precise specification of cell fate.