The Dynamic Spatial Structure of Flocks.

Studies of collective motion have heretofore been dominated by a thermodynamic perspective in which the emergent "flocked" phases are analyzed in terms of their time-averaged orientational and spatial properties. Studies that attempt to scrutinize the dynamical processes that spontaneously drive the formation of these flocks from initially random configurations are far more rare, perhaps owing to the fact that said processes occur far from the eventual long-time steady state of the system and thus lie outside the scope of traditional statistical mechanics. For systems whose dynamics are simulated numerically, the nonstationary distribution of system configurations can be sampled at different time points, and the time evolution of the average structural properties of the system can be quantified. In this paper, we employ this strategy to characterize the spatial dynamics of the standard Vicsek flocking model using two correlation functions common to condensed matter physics. We demonstrate, for modest system sizes with 800 to 2000 agents, that the self-assembly dynamics can be characterized by three distinct and disparate time scales that we associate with the corresponding physical processes of clustering (compaction), relaxing (expansion), and mixing (rearrangement). We further show that the behavior of these correlation functions can be used to reliably distinguish between phenomenologically similar models with different underlying interactions and, in some cases, even provide a direct measurement of key model parameters.

Postdoctoral researchers' perspectives on working conditions and equal opportunities in German academia.

Postdoctoral researchers (postdocs) are an essential component of the scientific workforce in German universities and research institutions and play a vital role in advancing knowledge and innovation. However, the experiences of postdocs and other early career researchers (ECRs) indicate that working conditions pose a significant challenge to the pursuit of a long-term research career in Germany-particularly for international scientists and those from marginalized groups. We examine how unstable working conditions as well as insufficient structural support for equal opportunities and diversity are significant obstacles for the career development of ECRs in German academia. We discuss these issues with the aid of an extensive survey recently conducted and published by PostdocNet, a target-group network representing the interests of postdocs across Germany's Max Planck Society. The survey drew responses from 659 postdoctoral researchers working at the Max Planck Society and represents one of the few datasets of postdoctoral researchers' perspectives in Germany. Building on these findings, we suggest actions at governmental, institutional, and individual levels to improve the working conditions of postdoctoral researchers in Germany.

QUANTUM OPTICS. Universal linear optics.

Linear optics underpins fundamental tests of quantum mechanics and quantum technologies. We demonstrate a single reprogrammable optical circuit that is sufficient to implement all possible linear optical protocols up to the size of that circuit. Our six-mode universal system consists of a cascade of 15 Mach-Zehnder interferometers with 30 thermo-optic phase shifters integrated into a single photonic chip that is electrically and optically interfaced for arbitrary setting of all phase shifters, input of up to six photons, and their measurement with a 12-single-photon detector system. We programmed this system to implement heralded quantum logic and entangling gates, boson sampling with verification tests, and six-dimensional complex Hadamards. We implemented 100 Haar random unitaries with an average fidelity of 0.999 ± 0.001. Our system can be rapidly reprogrammed to implement these and any other linear optical protocol, pointing the way to applications across fundamental science and quantum technologies.

Left atrial rupture secondary to myxomatous mitral valve disease in 11 dogs.

The purpose of this retrospective study was to evaluate the long-term outcome in dogs with left atrial rupture secondary to myxomatous mitral valve disease. Eleven client-owned dogs met the inclusion criteria for the study. Median age was 11.6 yr (range, 8.3-17.8 yr), and median weight was 5.8 kg (range, 3.8-15.2 kg). Of the 11 dogs, 10 survived the initial 24 hr after diagnosis and 5 of the dogs were still alive at the conclusion of data collection. The median survival of all dogs was 203 days. Dogs with no previous history of congestive heart failure (CHF) at the time of diagnosis had a significantly longer median survival time (345 days) compared with dogs with a previous history of CHF (160 days, P = 0.0038). Outcome of dogs with myxomatous mitral valve disease presenting with left atria rupture was more favorable than previously reported, and dogs without previous CHF survived the longest.

Constrictive pericarditis following surgical repair of a peritoneopericardial diaphragmatic hernia in a cat.

A 4-year-old female spayed domestic longhair cat was referred for dyspnea. Further diagnostics revealed severe pleural effusion and a peritoneopericardial diaphragmatic hernia (PPDH). Following surgical correction of the PPDH the pleural effusion persisted. Re-check echocardiogram 4 weeks after initial evaluation revealed leftward deviation of the interventricular septum and interatrial septum occurring with inspiration. There were also exaggerated phasic changes in trans-tricuspid flow velocities suggestive of constrictive pericardial disease. Cardiac catheterization was performed and revealed elevated pressures in the right atrium and right ventricle. Constrictive pericarditis (CP) and epicarditis was confirmed at surgery, where subtotal pericardiectomy was performed with epicardial decortication. The cat continued to develop recurrent pleural effusion after surgery, although the volume and frequency of recurrence slowed over time. This is the first reported case of CP following PPDH repair in a cat.

Characterization of polar membrane lipids of the extremely halophilic bacterium Salinibacter ruber and possible role of cardiolipin.

The lipid composition of the extremely halophilic bacterium Salinibacter ruber (Bacteroidetes) was investigated by thin layer chromatography, gas chromatography, high performance liquid chromatography and electrospray ionization-mass spectrometry. Polar lipids represent about 80% of the total lipid extract. The main polar lipids are a sulfonic acid analogue of ceramide (or capnine analogue), phosphatidylcholine, phosphatidylserine, dimethylphosphatidylethanolamine, phosphatidylglycerol, cardiolipin or bisphosphatidylglycerol, and a glycolipid. The major acyl chains in the phospholipids are C16:1 Delta9cis and C18:1 Delta11cis, while the sulfonolipid contains an amide-bound iso C15:0 fatty acid. On changing the salinity of the culture medium, no significant differences were found in the lipid profile or the unsaturation of the lipid fatty acyl chains. The structure of the cardiolipin, which represents 20% of polar lipids, has been elucidated by gas chromatography and electrospray ionization mass spectrometry analysis.

Pneumatosis coli in a dog.

A 17-year-old, castrated male Maltese was presented with chronic polyphagia and a 2-week history of tenesmus, diarrhea, hematochezia, weight loss, and ribbon-like feces. Pneumatosis coli was diagnosed by abdominal radiography. Concurrent hyperadrenocorticism was suspected. The clinical signs of colorectal disease resolved within 2 days of initiating a lowresidue diet and oral metronidazole. Pneumatosis coli should be considered as a differential diagnosis for colorectal disease in dogs.

Lymphangiosarcoma in two cats.

Lymphangiosarcoma is a malignant neoplasm of the lymphatic endothelium that is rare in cats. This report describes two cases of feline lymphangiosarcoma that originated in the distal limb, causing intractable lymphoedema and serosanguineous discharge with ecchymoses in local and distant sites. In association with the neoplasia, one cat had cortical bone lysis of multiple metacarpal bones of the affected limb and the other had severe immune-mediated haemolytic anaemia (IMHA). The disease in both cases affected young cats and progressed rapidly. Persistent distal limb lymphoedema with serosanguineous discharge is suggestive of lymphangiosarcoma especially when local or distal ecchymoses are evident.

Cold-active enzymes studied by comparative molecular dynamics simulation.

Enzymes from cold-adapted species are significantly more active at low temperatures, even those close to zero Celsius, but the rationale of this adaptation is complex and relatively poorly understood. It is commonly stated that there is a relationship between the flexibility of an enzyme and its catalytic activity at low temperature. This paper gives the results of a study using molecular dynamics simulations performed for five pairs of enzymes, each pair comprising a cold-active enzyme plus its mesophilic or thermophilic counterpart. The enzyme pairs included alpha-amylase, citrate synthase, malate dehydrogenase, alkaline protease and xylanase. Numerous sites with elevated flexibility were observed in all enzymes; however, differences in flexibilities were not striking. Nevertheless, amino acid residues common in both enzymes of a pair (not present in insertions of a structure alignment) are generally more flexible in the cold-active enzymes. The further application of principle component analysis to the protein dynamics revealed that there are differences in the rate and/or extent of opening and closing of the active sites. The results indicate that protein dynamics play an important role in catalytic processes where structural rearrangements, such as those required for active site access by substrate, are involved. They also support the notion that cold adaptation may have evolved by selective changes in regions of enzyme structure rather than in global change to the whole protein.

The influence of different temperature programmes on the bioremediation of polycyclic aromatic hydrocarbons (PAHs) in a coal-tar contaminated soil by in-vessel composting.

The biodegradation of 16 US. EPA-listed polycyclic aromatic hydrocarbons (sigma PAHs), with accompanying humification and microbial community structure changes during simulated in-vessel composting-bioremediation of an aged coal-tar-contaminated soil amended with green waste were studied over 56 days. The experimental design compared one constant temperature profile (TC=38 degrees C) with three variable temperature profiles (TP1, TP2 and TP3), including treatment at 70 degrees C to comply with regulatory requirements. Greatest sigma PAHs removal (75.4+/-0.1%; k(1)=0.026 day(-1), R(2)=0.98) occurred at TC=38 degrees C compared to all variable temperature profiles TP1 (62.1+/-11.0%; k(1)=0.016 day(-1), R(2)=0.93), TP2 (71.8+/-8.2%; k(1)=0.021 day(-1), R(2)=0.95) and TP3 (45.3+/-9.7%; k(1)=0.010 day(-1), R(2)=0.91). This study proved that using thermophilic temperatures (70 degrees C) towards the end of in-vessel composting processes (TP2) resulted in greater sigma PAHs removal than using other variable temperature profiles (TP1, TP3), as long as the increase was stepwise via an intermediate temperature (55 degrees C). Phospholipid fatty acid (PLFA) signatures indicated that use of thermophilic temperatures towards the end of the in-vessel composting-bioremediation (TP2) resulted in a higher fungal to bacterial PLFA ratio and a lower Gram-positive to Gram-negative (G(+)/G(-)) bacterial ratio. Fluorescence excitation-emission matrix (EEM) showed the presence of peaks typical of humic-like (Ex/Em wavelength pair approximately 340/460 nm) and fulvic-acid-like (Ex/Em wavelength pair approximately 245/460 nm) substances, indicating mineralization and/or maturation of the compost. Varying the temperature during in-vessel composting to comply with regulatory requirements for pathogen control, promoted contaminant biodegradation, microbial activity and compost maturation.

Phenotypic and genotypic characterisation of Bacillus cereus isolates from Bangladeshi rice.

We report the first phenotypic and genotypic characterisation of Bacillus cereus from Bangladeshi rice. Seven strains of B. cereus were isolated from two high-yielding rice varieties (BR5 and BRRI Dhan28) which are cultivated during different rice-growing seasons in Bangladesh. The strains were identified as B. cereus based on colonial and cellular (light microscopic) morphology and were confirmed using the API 50 CHB test system and 16S rDNA analysis. They could also be distinguished from each other based on their substrate-utilisation patterns using the API system. No psychrotrophic (cold-tolerant) isolates were obtained and all were mesophilic with a minimum growth temperature of 10 degrees C, but with an ability to grow at a higher rate than normal temperature (45 degrees C) for B. cereus. All strains had temperature optima between 35 and 45 degrees C, but two groups could be distinguished based on having either a narrow or a broad optimum range. The different strains could not be distinguished based on their phospholipid compositions including major fatty acyl chains which were typical for B. cereus. However, capillary-GC/MS analysis of trace fatty acyl components of the lipids has been used for the first time to group the isolates. Genotypic analysis of the rDNA region has also been used to distinguish the strains. Restriction fragment length polymorphism (RFLP) analysis of the spacer region between the 16S and 23S rRNA genes yielded two groups based on different base sequences, whereas sequence analysis of variable regions in the 16S rRNA gene gave four different groups by base differences at two positions. Despite their association with rice, none of the strains produced emetic toxin. The spore germination response of heat-activated spores of the Bangladeshi B. cereus strains was typical of the bacterium, but three different groups could be identified based on differences in germination rates. The use of this polyphasic approach to taxonomy has enabled all the B. cereus strains to be distinguished from each other.

Strains of Bacillus cereus vary in the phenotypic adaptation of their membrane lipid composition in response to low water activity, reduced temperature and growth in rice starch.

The phenotypic adaptation of membrane lipids in seven strains of the food-poisoning bacterium Bacillus cereus, isolated from Bangladeshi rice, is reported in relation to their ability to grow under conditions of low water activity (a(w)), reduced temperature and the presence of soluble rice starch. The strains have different membrane phospholipid head-group and fatty acyl compositions, and they display individual differences in their responses to both low a(w) and reduced temperature. The extent of the increase in anionic membrane lipids in response to low a(w) varies from strain to strain, is solute specific and in one strain does not occur. Growth is stimulated by the presence of soluble rice starch and results in a large rise in the proportion of diphosphatidylglycerol (DPG) at the expense of phosphatidylglycerol (PG), without any change in the proportion of total anionic phospholipids. Growth at 15 degrees C compared with 37 degrees C increases the proportions of DPG and phosphatidylethanolamine at the expense of PG. At the lower temperature there are changes in phospholipid fatty acyl composition characteristic of those expected to maintain membrane fluidity, including increases in the amount of total branched fatty acids and the anteiso-/iso-branched ratio, and a decrease in the equivalent chain-length, but there are strain differences in how those changes were achieved. In contrast to some other bacilli, there are persistent large increases in the proportions of unsaturated fatty acyl chains in phospholipids during growth at 15 degrees C.

Antarctic bacteria inhibit growth of food-borne microorganisms at low temperatures.

The aim of this study was to identify Antarctic microorganisms with the ability to produce cold-active antimicrobial compounds with potential for use in chilled food preservation. Colonies (4496) were isolated from 12 Antarctic soil samples and tested against Listeria innocua, Pseudomonas fragi and Brochothrix thermosphacta. Thirteen bacteria were confirmed as being growth-inhibitor producers (detection rate 0.29%). When tested against a wider spectrum of eight target organisms, some of the isolates also inhibited the growth of L. monocytogenes and Staphylococcus aureus. Six inhibitor producers were psychrotrophic (growth optima between 18 and 24 degrees C), halotolerant (up to 10% NaCl) and catalase-positive; all but one were Gram-positive and oxidase-positive. The inhibitors produced by four bacteria were sensitive to proteases, suggesting a proteinaceous nature. Four of the inhibitor-producers were shown to be species of Arthrobacter, Planococcus and Pseudomonas on the basis of their 16S rRNA gene sequences and fatty acid compositions. It was concluded that Antarctic soils represent an untapped reservoir of novel, cold-active antimicrobial-producers.

Rhodopseudomonas acidophila strain 10050 contains photosynthetic LH2 antenna complexes that are not enriched with phosphatidylglycerol, and the phospholipids have a fatty acyl composition that is unusual for purple non-sulfur bacteria.

The phospholipid composition of Rhodopseudomonas acidophila strain 10050 grown aerobically or anaerobically in the light was determined. The major phospholipids present in the aerobic cells were phosphatidylethanolamine (PE; 54%), phosphatidylglycerol (PG; 24%) and cardiolipin (diphosphatidylglycerol, DPG) (14%), together with phosphatidylcholine (PC; 5%). On moving the cells to anaerobic photosynthetic growth in the light PE remained the major phospholipid (37-49%), but there was a major change in the proportion of PC, which increased to 31-33%, and corresponding reductions in the contents of PG to 11-16% and DPG to 4-5%. The fatty acid composition of the phospholipids was unusual, compared with other purple non-sulfur photosynthetic bacteria, in that it contained 16:0 (29%), 17:1 (20%) and 19:1 (9%) plus several mainly unsaturated 2-OH fatty acids (9% total) as major components, when grown aerobically in the dark. In contrast when grown photosynthetically under anaerobic conditions there was <2% 17:1 or 19:1 present, while the amounts of 16:1 and 18:1 increased, and 16:0 decreased. The phospholipid composition of the purified light-harvesting complex 2 (LH2) complex was PE (43%), PC (42%) and DPG (15%). Unexpectedly, there was no PG associated with the purified LH2. These findings contrast with previous studies on several other photosynthetic bacteria, which had shown an increase in PG upon photosynthetic growth [Biochem. J. 181 (1979) 339]. The prior hypothesis that phosphatidylglycerol has some specific role to play in the function of light-harvesting complexes cannot be true for Rps. acidophila. It is suggested that specific integral membrane proteins may strongly influence the phospholipid content of the host membranes into which they are inserted.

Bacterial membranes: the effects of chill storage and food processing. An overview.

The shelf life of food is extended by refrigeration because the metabolic processes of food-associated microorganisms are slowed by the lowered temperature. Nonetheless, cold-adapted psychrotrophic food-poisoning and food-spoilage bacteria remain a concern because they possess cold-adapted proteins and membrane lipids that facilitate growth at low temperatures. The use of membrane-disrupting novel preservation techniques, such as ultrasound, high hydrostatic pressure or pulsed electric field, offer the potential for an extension of shelf life. This review considers the interacting and potentially synergistic effects of chill storage or mild heat treatment on membrane properties, with the disruptive effects of membrane-targeted physical treatments.

The Antarctic Psychrobacter sp. TAD1 has two cold-active glutamate dehydrogenases with different cofactor specificities. Characterisation of the NAD+-dependent enzyme.

Psychrobacter sp. TAD1 is a psychrotolerant bacterium from Antarctic frozen continental water that grows from 2 to 25 degrees C with optimal growth rate at 20 degrees C. The new isolate contains two glutamate dehydrogenases (GDH), differing in their cofactor specificities, subunit sizes and arrangements, and thermal properties. NADP+-dependent GDH is a hexamer of 47 kDa subunits and it is comparable to other hexameric GDHs of family-I from bacteria and lower eukaria. The NAD+-dependent enzyme, described in this communication, has a subunit weight of 160 kDa and belongs to the novel class of GDHs with large size subunits. The enzyme is a dimer; this oligomeric arrangement has not been reported previously for GDH. Both enzymes have an apparent optimum temperature for activity of approximately 20 degrees C, but their cold activities and thermal labilities are different. The NAD+-dependent enzyme is more cold active: at 10 C it retains 50% of its maximal activity, compared with 10% for the NADP+-dependent enzyme. The NADP+-dependent enzyme is more heat stable, losing only 10% activity after heating for 30 min, compared with 95% for the NAD+-dependent enzyme. It is concluded that in Psychrobacter sp. TAD1 not only does NAD+-dependent GDH have a novel subunit molecular weight and arrangement, but that its polypeptide chains are folded differently from those of NADP+-dependent GDH, providing different cold-active properties to the two enzymes.

Citrate synthase and 2-methylcitrate synthase: structural, functional and evolutionary relationships.

Following the complete sequencing of the Escherichia coli genome, it has been shown that the proposed second citrate synthase of this organism, recently described by the authors, is in fact a 2-methylcitrate synthase that possesses citrate synthase activity as a minor component. Whereas the hexameric citrate synthase is constitutively produced, the 2-methylcitrate synthase is induced during growth on propionate, and the catabolism of propionate to succinate and pyruvate via 2-methylcitrate is proposed. The citrate synthases of the psychrotolerant eubacterium DS2-3R, and of the thermophilic archaea Thermoplasma acidophilum and Pyrococcus furiosus, are approximately 40% identical in sequence to the Escherichia coli 2-methylcitrate synthase and also possess 2-methylcitrate synthase activity. The data are discussed with respect to the structure, function and evolution of citrate synthase and 2-methylcitrate synthase.

Re-evaluation of the hypothesis that biodegradable surfactants stimulate surface attachment of competent bacteria.

The hypothesis that biodegradable surfactants stimulate the attachment of biodegradation-competent bacteria to surfaces has been re-evaluated using a variant of the surfactant-degrading bacterium Pseudomonas sp. DES1 designated Pseudomonas sp. DES2. This variant was identical to the parental strain in terms of its carbon-utilization patterns and alcohol dehydrogenase and alkylsulfatase complements (enzymes involved in surfactant biodegradation), but differed markedly in its growth characteristics when using sodium dodecyl triethoxysulfate or triethylene glycol dodecyl ether as secondary carbon sources. Pseudomonas sp. DES1 exhibited diauxie in these surfactant-based culture media in contrast to Pseudomonas sp. DES2, which exhibited single-phase growth. Pseudomonas sp. DES2 did not attach to river sediment in a microcosm system when challenged with a dose of either surfactant, although it did biodegrade the substrate. In contrast, Pseudomonas sp. DES1 attached to the river sediment whilst biodegrading the test substrate. It is concluded that the ether-scission system, which is responsible for primary biodegradation of both substrates, is deregulated in Pseudomonas sp. DES2 in contrast to that in Pseudomonas sp. DES1, and that, contrary, to a previous hypothesis, biodegradable surfactants do not necessarily stimulate the attachment of biodegradation-competent bacteria during their biodegradation.