The Dimorphos ejecta plume properties revealed by LICIACube.

The Double Asteroid Redirection Test (DART) had an impact with Dimorphos (a satellite of the asteroid Didymos) on 26 September 20221. Ground-based observations showed that the Didymos system brightened by a factor of 8.3 after the impact because of ejecta, returning to the pre-impact brightness 23.7 days afterwards2. Hubble Space Telescope observations made from 15 minutes after impact to 18.5 days after, with a spatial resolution of 2.1 kilometres per pixel, showed a complex evolution of the ejecta3, consistent with other asteroid impact events. The momentum enhancement factor, determined using the measured binary period change4, ranges between 2.2 and 4.9, depending on the assumptions about the mass and density of Dimorphos5. Here we report observations from the LUKE and LEIA instruments on the LICIACube cube satellite, which was deployed 15 days in advance of the impact of DART. Data were taken from 71 seconds before the impact until 320 seconds afterwards. The ejecta plume was a cone with an aperture angle of 140 ± 4 degrees. The inner region of the plume was blue, becoming redder with increasing distance from Dimorphos. The ejecta plume exhibited a complex and inhomogeneous structure, characterized by filaments, dust grains and single or clustered boulders. The ejecta velocities ranged from a few tens of metres per second to about 500 metres per second.

Collisional formation of top-shaped asteroids and implications for the origins of Ryugu and Bennu.

Asteroid shapes and hydration levels can serve as tracers of their history and origin. For instance, the asteroids (162173) Ryugu and (101955) Bennu have an oblate spheroidal shape with a pronounced equator, but contain different surface hydration levels. Here we show, through numerical simulations of large asteroid disruptions, that oblate spheroids, some of which have a pronounced equator defining a spinning top shape, can form directly through gravitational reaccumulation. We further show that rubble piles formed in a single disruption can have similar porosities but variable degrees of hydration. The direct formation of top shapes from single disruption alone can explain the relatively old crater-retention ages of the equatorial features of Ryugu and Bennu. Two separate parent-body disruptions are not necessarily required to explain their different hydration levels.

The solar nebula origin of (486958) Arrokoth, a primordial contact binary in the Kuiper Belt.

The New Horizons spacecraft's encounter with the cold classical Kuiper Belt object (486958) Arrokoth (provisional designation 2014 MU69) revealed a contact-binary planetesimal. We investigated how Arrokoth formed and found that it is the product of a gentle, low-speed merger in the early Solar System. Its two lenticular lobes suggest low-velocity accumulation of numerous smaller planetesimals within a gravitationally collapsing cloud of solid particles. The geometric alignment of the lobes indicates that they were a co-orbiting binary that experienced angular momentum loss and subsequent merger, possibly because of dynamical friction and collisions within the cloud or later gas drag. Arrokoth's contact-binary shape was preserved by the benign dynamical and collisional environment of the cold classical Kuiper Belt and therefore informs the accretion processes that operated in the early Solar System.

Saturn's small inner satellites: clues to their origins.

Cassini images of Saturn's small inner satellites (radii of less than approximately 100 kilometers) have yielded their sizes, shapes, and in some cases, topographies and mean densities. This information and numerical N-body simulations of accretionary growth have provided clues to their internal structures and origins. The innermost ring-region satellites have likely grown to the maximum sizes possible by accreting material around a dense core about one-third to one-half the present size of the moon. The other small satellites outside the ring region either may be close to monolithic collisional shards, modified to varying degrees by accretion, or may have grown by accretion without the aid of a core. We derived viscosity values of 87 and 20 square centimeters per second, respectively, for the ring material surrounding ring-embedded Pan and Daphnis. These moons almost certainly opened their respective gaps and then grew to their present size early on, when the local ring environment was thicker than it is today.

RNA backbone rotamers--finding your way in seven dimensions.

Despite the importance of local structural detail for a mechanistic understanding of RNA catalysis and binding functions, RNA backbone conformation has been recalcitrant to analysis. There are too many variable dihedral angles per residue, and their raw empirical distributions are poorly clustered. This study applies quality-filtering techniques (using resolution, crystallographic B factor and all-atom-steric clashes) to the backbone dihedral angle distributions from a selected 8636 residue RNA database. With noise levels significantly decreased, clear signal appears for the underlying angle preferences. We analyse the multidimensional backbone dihedral distributions within sugar-to-sugar 'suites' rather than chemical residues due to the greater base interaction and steric interdependence within the suite. The final result is a small library of RNA backbone rotamers, each represented by a data cluster in seven-dimensional dihedral space, which should provide valid conformations for nearly all RNA backbones encountered in experimental structures. We are in the process of improving that library, and developing tools and applications for it in structure determination and analysis.

Biological variability in serum and urinary indices of bone formation and resorption in dogs.

Serum and urinary assays of bone markers provide a noninvasive alternative to bone biopsy in the study of bone metabolism in humans. Many of the commercial assays that were originally developed for use in humans have been shown to cross-react in dogs, and it should therefore be possible to use these assays to study bone remodeling in dogs. The interpretation of bone marker data in humans is hampered by extensive inter- and intra-subject variability. The specific aim of this study was therefore to determine the extent of biological variability in bone markers in dogs. Serum and urine samples were collected every 4 hours over a 24-hour period (short-term study), and every week over a 12-week period (long-term study). Serum bone-specific alkaline phosphatase (BALP) and urinary deoxypyridinoline (Dpd) and N-terminal telopeptide of collagen (NTx) were measured with commercial enzyme immunoassays. Serum osteocalcin (OC) and carboxyterminal crosslinked telopeptide of type I collagen (ICTP) were measured with commercial radioimmunoassays. In the short-term study, statistically significant diurnal rhythms were identified for OC, BALP, ICTP, and Dpd. No clear rhythm was evident for NTx. There was no evidence of statistically significant long-term variability in marker excretion over the 12 weeks. Our findings confirm the utility of these assays in dogs. However, as in humans, care must be taken to ensure that specimens are collected at a consistent time of day. Moreover, given the inherent variability in marker excretion in individual animals, the most appropriate use for these assays is as a screening tool for cohort studies, rather than as a diagnostic or prognostic tool in the individual animal.

Collisions and gravitational reaccumulation: forming asteroid families and satellites.

Numerical simulations of the collisional disruption of large asteroids show that although the parent body is totally shattered, subsequent gravitational reaccumulation leads to the formation of an entire family of large and small objects with dynamical properties similar to those of the parent body. Simulations were performed in two different collisional regimes representative of asteroid families such as Eunomia and Koronis. Our results indicate that all large family members must be made of gravitationally reaccumulated fragments; that the post-collision member size distribution and the orbital dispersion are steeper and smaller, respectively, than for the evolved families observed today; and that satellites form frequently around family members.

Evaluation of susceptibility testing to detect fluoroquinolone resistance mechanisms in Streptococcus pneumoniae.

To determine if susceptibility testing of Streptococcus pneumoniae could detect those isolates that had one of the recognized mechanisms of fluoroquinolone resistance, 101 isolates were selected; the levofloxacin MIC for 28 of these isolates was > or =4 microg/ml. Only isolates with both parC and gyrA mutations or with no recognized resistance mechanisms were reliably identified by using these results. Isolates with only a parC mutation could not be detected reliably using any susceptibility testing method.

Trimethoprim-sulfamethoxazole induced aseptic meningitis in a renal transplant patient.

A 45-year-old man underwent renal transplant for end-stage renal disease complicating systemic lupus erythematosis. Within 24 hours of initiating Pneumocystis carinii pneumonia (PCP) prophylaxis with trimethoprim-sulfamethoxazole (TMP-SMX) he developed fever and confusion. Cerebrospinal fluid examination revealed a pleocytosis but cultures were negative. The patient improved within three days after cessation of the TMP-SMX but symptoms recurred rapidly upon drug rechallenge. Drug-induced aseptic meningitis is an uncommon but well described clinical entity. This is the first case described in a patient following renal transplantation. The literature is reviewed and the clinical features, diagnostic challenges and possible mechanisms of TMP-SMX-induced aseptic meningitis are discussed. This problem may be more common in the transplant population than is recognized given the difficulty of diagnosis combined with the widespread use of TMP-SMX as PCP prophylaxis.

SymROP: ROP protein with identical helices redesigned by all-atom contact analysis and molecular dynamics.

Experience has shown that protein redesigns (using the backbone from a known protein structure) are far more likely to produce well-ordered, native-like structures than are true de novo designs. Therefore, to design a four-helix bundle made of identical short helices, we here proceed by an extensive redesign of the ROP protein. A fully symmetrical SymROP sequence derived from ROP was chosen by modeling ideal-geometry side chains, including hydrogens, while maintaining the "goodness-of-fit" of side-chain packing by calculating all-atom contact surfaces with the Reduce and Probe programs. To estimate the probable extent of backbone movement and side-chain mobility, restrained molecular dynamics simulations were compared for candidate sequences and controls, including substitution of Abu for all or half the core Ala residues. The resulting 17-residue designed sequence is 41% identical to the relevant regions in ROP. SymROP is intended for construction by the Template Assembled Synthetic Proteins approach, to control the bundle topology, to use short helices, and to allow blocked termini and unnatural amino acids. ROP protein has been a valuable system for studying helical protein structure because of its simplicity and regularity within a structure large enough to have a real hydrophobic core. The SymROP design carries that simplicity and regularity even further.

Urinary markers of type I collagen degradation in the dog.

Urinary assays for type I collagen metabolites provide a non invasive index of bone resorption in humans, and are widely used in the management of patients with metabolic bone diseases. The specific aims of this study were to investigate the feasibility of using commercial human assay kits for quantifying the urinary excretion of type I collagen metabolites in dogs of different ages. Urine and serum samples were collected from 35 beagle dogs in five age groups (0 to 1 years; 1 to 2 years; 2 to 3 years; 3 to 7 years; > 8 years old). Urinary concentrations of pyridinoline (Pyd), deoxypyridinoline (Dpd), and the carboxy- and amino-terminal cross-linked telopeptides of type I collagen (CTx and NTx, respectively) were measured with commercial enzyme-linked immunoassay kits. Serum concentrations of another type I collagen metabolite, the carboxy-terminal cross-linked teloptide of type I collagen (ICTP), were measured with a commercial radioimmunoassay. Dilutional studies indicated that the four urinary assays show specific cross-reactivity with canine urine. Age-related differences in urinary marker excretion were identified, with young dogs excreting the highest concentrations of Pyd, Dpd, NTx and CTx. The correlation between the individual urinary markers was excellent (r = 0.87 to 0.98), while the correlation between serum ICTP and individual urinary markers was weaker (r = 0.52 to 0.64). These results validate the usefulness of the commercial assay kits in monitoring type I collagen metabolism in dogs. Histomorphometric studies have confirmed the relationship between collagen degradation and bone resorption in humans, and similar studies are now needed in dogs.

Representation, space and Hollywood Squares: looking at things that aren't there anymore.

It has been argued that the human cognitive system is capable of using spatial indexes or oculomotor coordinates to relieve working memory load (Ballard, D. H., Hayhoe, M. M., Pook, P. K., & Rao, R. P. N. (1997). Behavioral and Brain Sciences, 20(4), 723), track multiple moving items through occlusion (Scholl, D. J., & Pylyshyn, Z. W. (1999). Cognitive Psychology, 38, 259) or link incompatible cognitive and sensorimotor codes (Bridgeman, B., & Huemer, V. (1998). Consciousness and Cognition, 7, 454). Here we examine the use of such spatial information in memory for semantic information. Previous research has often focused on the role of task demands and the level of automaticity in the encoding of spatial location in memory tasks. We present five experiments where location is irrelevant to the task, and participants' encoding of spatial information is measured implicitly by their looking behavior during recall. In a paradigm developed from Spivey and Geng (Spivey, M. J., & Geng, J. (2000). submitted for publication), participants were presented with pieces of auditory, semantic information as part of an event occurring in one of four regions of a computer screen. In front of a blank grid, they were asked a question relating to one of those facts. Under certain conditions it was found that during the question period participants made significantly more saccades to the empty region of space where the semantic information had been previously presented. Our findings are discussed in relation to previous research on memory and spatial location, the dorsal and ventral streams of the visual system, and the notion of a cognitive-perceptual system using spatial indexes to exploit the stability of the external world.

A comparison of two techniques for the determination of serum bone-specific alkaline phosphatase activity in dogs.

Bone-specific alkaline phosphatase (BALP) shows potential as a marker of bone formation in the dog. Recent studies have indicated that serum BALP may provide a useful, non-invasive indicator of skeletal health in dogs, and as a diagnostic and prognostic marker in the management of dogs with musculoskeletal or metabolic disorders. Two assay techniques (one based on wheatgerm lectin precipitation followed by a simple enzymatic reaction, the second on a specific enzyme-linked immunoassay) were used to measure serum levels of BALP in 35 dogs of different ages. As expected, BALP concentrations decreased with age. For the enzymatic assay, mean (+/-SD) serum concentrations of BALP activities were 100.3 (+/-11.6) U/liter in dogs under 1 year of age, 25.3 (+/-6.8) U/L in dogs 1 to 2 years of age, 16.5 (+/-7.3) U/L in dogs 2 to 3 years of age, 14.3 (+/-5.6) U/L in dogs 3 to 7 years of age, and 12.3 (+/-4.8) U/L in dogs aged 8 years and older. Corresponding results from the immunoassay were 56.3 (+/-9.8) U/L, 10.7 (+/-4.5) U/L, 7.0 (+/-2.5) U/L, 6.7 (+/-3.6) U/L and 7.0 (+/-2.9) U/L. There was excellent correlation between the results from the two assay techniques (r = 0. 96; P < 0.0001). The correlation between BALP and total ALP activities was poor (r = 0.20 for enzymatic BALP, r = 0.31 for immunoreactive BALP), indicating that total ALP should be considered unreliable as an indicator of BALP activity in canine serum. The immunoassay demonstrated acceptable (13 per cent) cross-reactivity with the liver isoform of ALP. The commercial immunoassay kit is simple and provides fast results. Although the wheatgerm lectin/enzymatic technique is preferred in situations where the activities of all three isoforms of ALP are required, the immunoassay should be considered whenever the activity of BALP is the focus of interest.

The penultimate rotamer library.

All published rotamer libraries contain some rotamers that exhibit impossible internal atomic overlaps if built in ideal geometry with all hydrogen atoms. Removal of uncertain residues (mainly those with B-factors >/=40 or van der Waals overlaps >/=0.4 A) greatly improves the clustering of rotamer populations. Asn, Gln, or His side chains additionally benefit from flipping of their planar terminal groups when required by atomic overlaps or H-bonding. Sensitivity to skew and to the boundaries of chi angle bins is avoided by using modes rather than traditional mean values. Rotamer definitions are listed both as the modal values and in a preferred version that maximizes common atoms between related rotamers. The resulting library shows significant differences from previous ones, differences validated by considering the likelihood of systematic misfitting of models to electron density maps and by plotting changes in rotamer frequency with B-factor. Few rotamers now show atomic overlaps in ideal geometry; those overlaps are relatively small and can be understood in terms of bond angle distortions compensated by favorable interactions. The new library covers 94.5% of examples in the highest quality protein data with 153 rotamers and can make a significant contribution to improving the accuracy of new structures. Proteins 2000;40:389-408.

Exploring steric constraints on protein mutations using MAGE/PROBE.

When planning a mutation to test some hypothesis, one crucial question is whether the new side chain is compatible with the existing structure; only if it is compatible can the interpretation of mutational results be straightforward. This paper presents a simple way of using the sensitive geometry of all-atom contacts (including hydrogens) to answer that question. The interactive MAGE/PROBE system lets the biologist explore conformational space for the mutant side chain, with an interactively updated kinemage display of its all-atom contacts to the original structure. The Autobondrot function in PROBE systematically explores that same conformational space, outputting contact scores at each point, which are then contoured and displayed. These procedures are applied here in two types of test cases, with known mutant structures. In ricin A chain, the ability of a neighboring glutamate to rescue activity of an active-site mutant is modeled successfully. In T4 lysozyme, six mutations to Leu are analyzed within the wild-type background structure, and their Autobondrot score maps correctly predict whether or not their surroundings must shift significantly in the actual mutant structures; interactive examination of contacts for the conformations involved explains which clashes are relieved by the motions. These programs are easy to use, are available free for UNIX or Microsoft Windows operating systems, and should be of significant help in choosing good mutation experiments or in understanding puzzling results.

Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering.

Previous rotamer libraries showed little significant clustering for asparagine chi2 or glutamine chi3 values, but none of those studies corrected amide orientations or omitted disordered side chains. The current survey used 240 proteins at /=0.4 A). All H atoms were added and optimized, and amide orientation was flipped by 180 degrees if required by H bonding or atomic clashes. A side chain was included only if its amide orientation was clearly determined and if no atom had a B factor >/=40, alternate conformation, or severe clash; that selection process yielded 1,490 Asn and 863 Gln side chains. Clear clustering was observed for Asn chi2 and Gln chi3 (except when Gln chi2 is trans). For Gln, five major and four minor rotamers cover 87% of examples. For Asn, there are seven backbone-independent rotamers covering 94% of examples plus rotamers specified for strictly alpha-helical, beta, and left-handed (+phi) Asn. Although the strongest influence on chi angles is avoidance of atomic clashes (especially with the NH2 hydrogens), some Asn or Gln rotamers are influenced by favorable van der Waals contacts and others by specific local H-bond patterns.

Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms.

The technique of small-probe contact dot surfaces is described as a method for calculating and displaying the detailed atomic contacts inside or between molecules. It allows one both to measure and to visualize directly the goodness-of-fit of packing interactions. It requires both highly accurate structures and also the explicit inclusion of all hydrogen atoms and their van der Waals interactions. A reference dataset of 100 protein structures was chosen on the basis of resolution (1.7 A or better), crystallographic R-value, non-homology, and the absence of any unusual problems. Hydrogen atoms were added in standard geometry and, where needed, with rotational optimization of OH, SH, and NH+3 positions. Side-chain amide orientations were corrected where required by NH van der Waals clashes, as described in the accompanying paper. It was determined that, in general, methyl groups pack well in the default staggered conformation, except for the terminal methyl groups of methionine residues, which required rotational optimization. The distribution of serious clashes (i.e. non-H-bond overlap of >/=0.4 A) was studied as a function of resolution, alternate conformations, and temperature factor (B), leading to the decision that packing and other structural features would not be analyzed for residues in 'b' alternate conformations or with B-factors of 40 or above. At the level of the fine details analyzed here, structural accuracy improves quite significantly over the range from 1.7 to 1.0 A resolution. These high-resolution structures show impressively well-fitted packing interactions, with some regions thoroughly interdigitated and other regions somewhat sparser. Lower-resolution structures or model structures could undoubtedly be improved in accuracy by the incorporation of this additional information: for example, nucleic acid structures in non-canonical conformations are often very accurate for the bases and much less reliable for the backbone, whose conformation could be specified better by including explicit H atom geometry and contacts. The contact dots are an extremely sensitive method of finding problem areas, and often they can suggest how to make improvements. They can also provide explanations for structural features that have been described only as empirical regularities, which is illustrated by showing that the commonest rotamer of methionine (a left-handed spiral, with all chi values near -60 degrees) is preferred because it provides up to five good H atom van der Waals contacts. This methodology is thus applicable in two different ways: (1) for finding and correcting errors in structure models (either experimental or theoretical); and (2) for analyzing interaction patterns in the molecules themselves.

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation.

Small-probe contact dot surface analysis, with all explicit hydrogen atoms added and their van der Waals contacts included, was used to choose between the two possible orientations for each of 1554 asparagine (Asn) and glutamine (Gln) side-chain amide groups in a dataset of 100 unrelated, high-quality protein crystal structures at 0.9 to 1.7 A resolution. For the movable-H groups, each connected, closed set of local H-bonds was optimized for both H-bonds and van der Waals overlaps. In addition to the Asn/Gln "flips", this process included rotation of OH, SH, NH3+, and methionine methyl H atoms, flip and protonation state of histidine rings, interaction with bound ligands, and a simple model of water interactions. However, except for switching N and O identity for amide flips (or N and C identity for His flips), no non-H atoms were shifted. Even in these very high-quality structures, about 20 % of the Asn/Gln side-chains required a 180 degrees flip to optimize H-bonding and/or to avoid NH2 clashes with neighboring atoms (incorporating a conservative score penalty which, for marginal cases, favors the assignment in the original coordinate file). The programs Reduce, Probe, and Mage provide not only a suggested amide orientation, but also a numerical score comparison, a categorization of the marginal cases, and a direct visualization of all relevant interactions in both orientations. Visual examination allowed confirmation of the raw score assignment for about 40 % of those Asn/Gln flips placed within the "marginal" penalty range by the automated algorithm, while uncovering only a small number of cases whose automated assignment was incorrect because of special circumstances not yet handled by the algorithm. It seems that the H-bond and the atomic-clash criteria independently look at the same structural realities: when both criteria gave a clear answer they agreed every time. But consideration of van der Waals clashes settled many additional cases for which H-bonding was either absent or approximately equivalent for the two main alternatives. With this extra information, 86 % of all side-chain amide groups could be oriented quite unambiguously. In the absence of further experimental data, it would probably be inappropriate to assign many more than this. Some of the remaining 14 % are ambiguous because of coordinate error or inadequacy of the theoretical model, but the great majority of ambiguous cases probably occur as a dynamic mix of both flip states in the actual protein molecule. The software and the 100 coordinate files with all H atoms added and optimized and with amide flips corrected are publicly available.

Serum markers of bone metabolism in dogs.

OBJECTIVE: To establish reference values for a panel of serum markers of bone turnover in dogs of various ages. ANIMALS: Dogs in 4 age groups (0 to 1 year; 1 to 2 years; 3 to 7 years; > 8 years). PROCEDURE: Serum concentrations of the carboxyterminal propeptide of type-I procollagen (PICP) and the aminoterminal propeptide of type-I procollagen (PINP), both markers of type-I collagen synthesis (hence, bone formation), were measured by use of commercial human radioimmunoassay kits. Serum concentrations of the carboxyterminal cross-linked telopeptide of type-I collagen (ICTP), a marker for type-I collagen breakdown (hence, bone resorption), also were measured by use of a commercial human radioimmunoassay kit. Serum osteocalcin (OC) concentrations and alkaline phosphatase (ALP) isoenzyme activities were measured by use of techniques developed specifically for dogs. RESULTS: As expected, the highest values for all of the markers were found in young dogs (< 12 months old). Concentrations of OC and ICTP decreased with age, and were lowest in dogs > 8 years old. Total ALP and bone-specific ALP activities initially decreased with age, then increased in dogs > 8 years old. CONCLUSIONS AND CLINICAL RELEVANCE: Serum markers of bone turnover may be useful diagnostic and prognostic tools for management of dogs with musculoskeletal disorders.