Femtosecond X-ray protein nanocrystallography

X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (～200?nm to 2?μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.     

Initial genome sequencing and analysis of multiple myeloma

Multiple myeloma is an incurable malignancy of plasma cells, and its pathogenesis is poorly understood. Here we report the massively parallel sequencing of 38 tumour genomes and their comparison to matched normal DNAs. Several new and unexpected oncogenic mechanisms were suggested by the pattern of somatic mutation across the data set. These include the mutation of genes involved in protein translation (seen in nearly half of the patients), genes involved in histone methylation, and genes involved in blood coagulation. In addition, a broader than anticipated role of NF-κB signalling was indicated by mutations in 11 members of the NF-κB pathway. Of potential immediate clinical relevance, activating mutations of the kinase BRAF were observed in 4% of patients, suggesting the evaluation of BRAF inhibitors in multiple myeloma clinical trials. These results indicate that cancer genome sequencing of large collections of samples will yield new insights into cancer not anticipated by existing knowledge.     

A new terrestrial planarian species of the genus Marionfyfea (Platyhelminthes: Tricladida) found in Europe

Small (c. 1 cm long) terrestrial planarians found in the United Kingdom, the Netherlands and France are described as a new species, Marionfyfea adventor sp. nov. Individuals of the new species have a patchy brown external appearance with small, seemingly random pale blue-ish patches. They have multiple eyes, uniserial around the anterior end, biserial or triserial laterally for a short distance then sparsely uniserial and lateral to the posterior end. The anatomy is characterized by five or six pairs of ventral testes and a single pair of ovaries adjacent to the pharyngeal pouch. The base of each ovary is surrounded by parovarian cells. The penis is of the inverted type with a basal hemispherical seminal vesicle. Two adenodactyls, one ventral, one dorsal, are present in the common antrum. The only other known species of Marionfyfea is recorded only from the Auckland Islands, New Zealand and we assume that the new species has been introduced to Europe.

http://zoobank.org/urn:lsid:zoobank.org:pub:7AC3D565-0BEB-4B67-8BEC-11A13A70D663     

Tycho brahe in china: the Jesuit mission to Peking and the iconography of European instrument-making processes

In the late 1660s, Ferdinand Verbiest, a Flemish Jesuit missionary in Peking, was instructed to re-equip the Imperial Observatory. The new instruments which he caused to be built were modelled neither upon contemporary European prototypes, nor those of traditional Chinese astronomy, but on the pieces in Tycho Brahe's Mechanica, of eighty years before. The Chinese instruments were lavishly illustrated, moreover, in 105 woodcuts that contained detailed representations of their processes of construction. It is argued that these illustrations not only give us valuable insights into what the technical Jesuits did in Peking, but show how sixteenth- and seventeenth-century European craftsmen constructed their instruments, for while the location was Oriental, the technology was Western. They can also give important insights into how Tycho's prototypes had been built, and provide us with useful information regarding European instrument-making technology.     

Review of the harvest mice (genus Reithrodontomys ) in the Mexican state of México

We examined 590 specimens of Reithrodontomys from 95 localities in the state of México. Four species of the subgenus Reithrodontomys and 1 of the subgenus Aporodon were identified. The former subgenus included R. chrysopsis , R. sumichrasti , R. megalotis , and R. fulvescens , which has 2 subspecies— R. f. toltecus and R. f. mustelinus — in the state. The representative of the subgenus Aporodon is R. microdon wagner , which is recorded for the first time in the state. We give information on taxonomy, morphometrics, reproduction, habitat characteristics, and related fauna. A discriminant analysis correctly classified 100% of specimens from the 6 taxa with 5 canonical variates, and accounted for 96.1% of the variance with the first 3 canonical variates.     

Characterization of a contact zone between two subspecies of the big brown bat ( Eptesicus fuscus ) in Nebraska

Two subspecies of the big brown bat ( Eptesicus fuscus ) are reported to occur in Nebraska. The eastern race, E. f. fuscus , is reportedly bigger and darker than its western counterpart E. f. pallidus . Where these 2 subspecies come in contact is the subject of debate. We used external, cranial, and colorimetric data to investigate geographic variation among populations of E. fuscus in Nebraska to determine the location of the zone of contact between E. f. fuscus and E. f. pallidus . We discovered significant variation in external, cranial, and colorimetric data, suggesting that E. fuscus is represented by 2 subspecies in Nebraska. Our results showed that E. f. pallidus is smaller, possesses lighter pelage, and is restricted to the northern and western parts of Nebraska, whereas E. f. fuscus is larger, possesses darker pelage, and occurs in southern and southeastern parts of the state. Populations located between these regions represent intergrades of the 2 subspecies. We suggest that the subspecific boundary represents a broad zone of integration running in a northeast to southwest direction and may reflect the position of temperature and precipitation clines.     

Ocular dominance shift in kitten visual cortex caused by imbalance in retinal electrical activity

Monocular lid suture during the sensitive period early in the life of a kitten disrupts normal development of inputs from the two eyes to the visual cortex, causing a decrease in the fraction of cortical cells responding to the deprived eye. Such an ocular dominance shift has been assumed to depend on patterned visual experience, because no change in cortical physiology is produced by inequalities between the two eyes in retinal illumination or temporally modulated diffuse light stimulation. A higher-level process, involving gating signals from areas outside striate cortex, has been proposed to ensure that sustained changes in synaptic efficacy occur only in response to behaviourally significant visual inputs. To test whether such a process is necessary for ocular dominance plasticity, we treated 4-week-old kittens with visual deprivation and monocular tetrodotoxin (TTX) injections to create an imbalance in the electrical activities of the two retinas in the absence of patterned vision. After 1 week of treatment we determined the ocular dominance distribution of single units in primary visual cortex. In all kittens studied, a significant ocular dominance shift was found. In addition to this physiological change, there was an anatomical change in the lateral geniculate nucleus, where cells were larger in laminae receiving input from the more active eye. Our results indicate that patterned vision is not necessary for visual cortical plasticity, and that an imbalance in spontaneous retinal activity alone can produce a significant ocular dominance shift.     

Substrate-targeting gamma-secretase modulators

Selective lowering of Abeta42 levels (the 42-residue isoform of the amyloid-beta peptide) with small-molecule gamma-secretase modulators (GSMs), such as some non-steroidal anti-inflammatory drugs, is a promising therapeutic approach for Alzheimer's disease. To identify the target of these agents we developed biotinylated photoactivatable GSMs. GSM photoprobes did not label the core proteins of the gamma-secretase complex, but instead labelled the beta-amyloid precursor protein (APP), APP carboxy-terminal fragments and amyloid-beta peptide in human neuroglioma H4 cells. Substrate labelling was competed by other GSMs, and labelling of an APP gamma-secretase substrate was more efficient than a Notch substrate. GSM interaction was localized to residues 28-36 of amyloid-beta, a region critical for aggregation. We also demonstrate that compounds known to interact with this region of amyloid-beta act as GSMs, and some GSMs alter the production of cell-derived amyloid-beta oligomers. Furthermore, mutation of the GSM binding site in the APP alters the sensitivity of the substrate to GSMs. These findings indicate that substrate targeting by GSMs mechanistically links two therapeutic actions: alteration in Abeta42 production and inhibition of amyloid-beta aggregation, which may synergistically reduce amyloid-beta deposition in Alzheimer's disease. These data also demonstrate the existence and feasibility of 'substrate targeting' by small-molecule effectors of proteolytic enzymes, which if generally applicable may significantly broaden the current notion of 'druggable' targets.     

Melanopsin cells are the principal conduits for rod-cone input to non-image-forming vision

Rod and cone photoreceptors detect light and relay this information through a multisynaptic pathway to the brain by means of retinal ganglion cells (RGCs). These retinal outputs support not only pattern vision but also non-image-forming (NIF) functions, which include circadian photoentrainment and pupillary light reflex (PLR). In mammals, NIF functions are mediated by rods, cones and the melanopsin-containing intrinsically photosensitive retinal ganglion cells (ipRGCs). Rod-cone photoreceptors and ipRGCs are complementary in signalling light intensity for NIF functions. The ipRGCs, in addition to being directly photosensitive, also receive synaptic input from rod-cone networks. To determine how the ipRGCs relay rod-cone light information for both image-forming and non-image-forming functions, we genetically ablated ipRGCs in mice. Here we show that animals lacking ipRGCs retain pattern vision but have deficits in both PLR and circadian photoentrainment that are more extensive than those observed in melanopsin knockouts. The defects in PLR and photoentrainment resemble those observed in animals that lack phototransduction in all three photoreceptor classes. These results indicate that light signals for irradiance detection are dissociated from pattern vision at the retinal ganglion cell level, and animals that cannot detect light for NIF functions are still capable of image formation.