Recommended rejection of the names Malacoplasma gen. nov., Mesomycoplasma gen. nov., Metamycoplasma gen. nov., Metamycoplasmataceae fam. nov., Mycoplasmoidaceae fam. nov., Mycoplasmoidales ord. nov., Mycoplasmoides gen. nov., Mycoplasmopsis gen. nov. [Gupta, Sawnani, Adeolu, Alnajar and Oren 2018] and all proposed species comb. nov. placed therein.

The consensus of the members of the International Committee on Systematics of Prokaryotes' Subcommittee on the taxonomy of Mollicutes is that recently proposed sweeping changes to nomenclature of members of the Mycoplasmatales, specifically involving introduction of the names Malacoplasma gen. nov., Mesomycoplasma gen. nov., Metamycoplasma gen. nov., Metamycoplasmataceaefam. nov., Mycoplasmoidaceaefam. nov., Mycoplasmoidalesord. nov., Mycoplasmoides gen. nov., Mycoplasmopsis gen. nov., and all proposed species or subspecies comb. nov. placed therein, should be rejected because they violate one or more essential points of the International Code of Nomenclature of Prokaryotes.

ARID1B, a member of the human SWI/SNF chromatin remodeling complex, exhibits tumour-suppressor activities in pancreatic cancer cell lines.

BACKGROUND: The human ATP-dependent SWItch/sucrose nonfermentable (SWI/SNF) complex functions as a primary chromatin remodeler during ontogeny, as well as in adult life. Several components of the complex have been suggested to function as important regulators of tumorigenesis in various cancers. In the current study, we have characterised a possible tumour suppressor role for the largest subunit of the complex, namely the AT-rich interaction domain 1B (ARID1B). METHODS: We performed Azacytidine and Trichostatin A treatments, followed by bisulphite sequencing to determine the possible DNA methylation-induced transcription repression of the gene in pancreatic cancer (PaCa) cell lines. Functional characterisation of effect of ARID1B ectopic expression in MiaPaCa2 PaCa cell line, which harboured ARID1B homozygous deletion, was carried out. Finally, we evaluated ARID1B protein expression in pancreatic tumour samples using immunohistochemistry on a tissue microarray. RESULTS: ARID1B was transcriptionally repressed due to promoter hypermethylation, and ectopic expression severely compromised the ability of MiaPaCa2 cells to form colonies in liquid culture and soft agar. In addition, ARID1B exhibited significantly reduced/loss of expression in PaCa tissue, especially in samples from advanced-stage tumours, when compared with normal pancreas. CONCLUSION: The results therefore suggest a possible tumour-suppressor function for ARID1B in PaCa, thus adding to the growing list of SWI/SNF components with a similar function. Given the urgent need to design efficient targeted therapies for PaCa, our study assumes significance.

Genotype List String: a grammar for describing HLA and KIR genotyping results in a text string.

Knowledge of an individual's human leukocyte antigen (HLA) genotype is essential for modern medical genetics, and is crucial for hematopoietic stem cell and solid-organ transplantation. However, the high levels of polymorphism known for the HLA genes make it difficult to generate an HLA genotype that unambiguously identifies the alleles that are present at a given HLA locus in an individual. For the last 20 years, the histocompatibility and immunogenetics community has recorded this HLA genotyping ambiguity using allele codes developed by the National Marrow Donor Program (NMDP). While these allele codes may have been effective for recording an HLA genotyping result when initially developed, their use today results in increased ambiguity in an HLA genotype, and they are no longer suitable in the era of rapid allele discovery and ultra-high allele polymorphism. Here, we present a text string format capable of fully representing HLA genotyping results. This Genotype List (GL) String format is an extension of a proposed standard for reporting killer-cell immunoglobulin-like receptor (KIR) genotype data that can be applied to any genetic data that use a standard nomenclature for identifying variants. The GL String format uses a hierarchical set of operators to describe the relationships between alleles, lists of possible alleles, phased alleles, genotypes, lists of possible genotypes, and multilocus unphased genotypes, without losing typing information or increasing typing ambiguity. When used in concert with appropriate tools to create, exchange, and parse these strings, we anticipate that GL Strings will replace NMDP allele codes for reporting HLA genotypes.

Uniquely localized intra-molecular amino acid concentrations at the glycolytic enzyme catalytic/active centers of Archaea, Bacteria and Eukaryota are associated with their proposed temporal appearances on earth.

The distributions of amino acids at most-conserved sites nearest catalytic/active centers (C/AC) in 4,645 sequences of ten enzymes of the glycolytic Embden-Meyerhof-Parnas pathway in Archaea, Bacteria and Eukaryota are similar to the proposed temporal order of their appearance on Earth. Glycine, isoleucine, leucine, valine, glutamic acid and possibly lysine often described as prebiotic, i.e., existing or occurring before the emergence of life, were localized in positional and conservational defined aggregations in all enzymes of all Domains. The distributions of all 20 biologic amino acids in most-conserved sites nearest their C/ACs were quite different either from distributions in sites less-conserved and further from their C/ACs or from all amino acids regardless of their position or conservation. The major concentrations of glycine, e.g., perhaps the earliest prebiotic amino acid, occupies ≈ 16 % of all the most-conserved sites within a volume of ≈ 7-8 Å radius from their C/ACs and decreases linearly towards the molecule's peripheries. Spatially localized major concentrations of isoleucine, leucine and valine are in the mid-conserved and mid-distant sites from their C/ACs in protein interiors. Lysine and glutamic acid comprise ≈ 25-30 % of all amino acids within an irregular volume bounded by ≈ 24-28 Å radii from their C/ACs at the most-distant least-conserved sites. The unreported characteristics of these amino acids: their spatially and conservationally identified concentrations in Archaea, Bacteria and Eukaryota, suggest some common structural organization of glycolytic enzymes that may be relevant to their evolution and that of other proteins. We discuss our data in relation to enzyme evolution, their reported prebiotic putative temporal appearances on Earth, abundances, biological "cost", neighbor-sequence preferences or "ordering" and some thermodynamic parameters.

Genome-wide analysis of DNA copy-number changes using cDNA microarrays.

Gene amplifications and deletions frequently contribute to tumorigenesis. Characterization of these DNA copy-number changes is important for both the basic understanding of cancer and its diagnosis. Comparative genomic hybridization (CGH) was developed to survey DNA copy-number variations across a whole genome. With CGH, differentially labelled test and reference genomic DNAs are co-hybridized to normal metaphase chromosomes, and fluorescence ratios along the length of chromosomes provide a cytogenetic representation of DNA copy-number variation. CGH, however, has a limited ( approximately 20 Mb) mapping resolution, and higher-resolution techniques, such as fluorescence in situ hybridization (FISH), are prohibitively labour-intensive on a genomic scale. Array-based CGH, in which fluorescence ratios at arrayed DNA elements provide a locus-by-locus measure of DNA copy-number variation, represents another means of achieving increased mapping resolution. Published array CGH methods have relied on large genomic clone (for example BAC) array targets and have covered only a small fraction of the human genome. cDNAs representing over 30,000 radiation-hybrid (RH)-mapped human genes provide an alternative and readily available genomic resource for mapping DNA copy-number changes. Although cDNA microarrays have been used extensively to characterize variation in human gene expression, human genomic DNA is a far more complex mixture than the mRNA representation of human cells. Therefore, analysis of DNA copy-number variation using cDNA microarrays would require a sensitivity of detection an order of magnitude greater than has been routinely reported. We describe here a cDNA microarray-based CGH method, and its application to DNA copy-number variation analysis in breast cancer cell lines and tumours. Using this assay, we were able to identify gene amplifications and deletions genome-wide and with high resolution, and compare alterations in DNA copy number and gene expression.

Randomized clinical trial of fluid restriction in colorectal surgery.

BACKGROUND: Perioperative fluid therapy can influence postoperative hospital stay and complications after elective colorectal surgery. This trial was designed to examine whether an extremely restricted perioperative fluid protocol would reduce hospital stay beyond the existing fast-track hospital time of 7 days after surgery. METHODS: Patients were randomized to restricted or standard perioperative intravenous fluid regimens in a single-centre trial. Randomization was stratified for colonic, rectal, open and laparoscopic surgery. Patients were all treated within a fast-track protocol (careful preoperative preparation, optimal analgesia, early oral nutrition and early mobilization). The primary endpoint was length of postoperative hospital stay. The secondary endpoint was complications within 30 days. RESULTS: Seventy-nine patients were randomized to restricted and 82 to standard fluid therapy. Patients in the restricted group received a median of 3050 ml fluid on the day of surgery compared with 5775 ml in the standard group (P < 0·001). There was no difference between groups in primary hospital stay (median 6·0 days in both groups; P = 0·194) or stay including readmission (median 6·0 days in both groups; P = 0·158). The proportion of patients with complications was significantly lower in the restricted group (31 of 79 versus 47 of 82; P = 0·027). Vasopressors were more often required in the restricted group (97 versus 80 per cent; P < 0·001). CONCLUSION: Restricted perioperative intravenous fluid administration does not reduce length of stay in a fast-track protocol.

New Ameloblastoma Cell Lines Enable Preclinical Study of Targeted Therapies.

Ameloblastoma (AB) is an odontogenic tumor that arises from ameloblast-lineage cells. Although relatively uncommon and rarely metastatic, AB tumors are locally invasive and destructive to the jawbone and surrounding structures. Standard-of-care surgical resection often leads to disfigurement, and many tumors will locally recur, necessitating increasingly challenging surgeries. Recent genomic studies of AB have uncovered oncogenic driver mutations, including in the mitogen-activated protein kinase (MAPK) and Hedgehog signaling pathways. Medical therapies targeting those drivers would be a highly desirable alternative or addition to surgery; however, a paucity of existing AB cell lines has stymied clinical translation. To bridge this gap, here we report the establishment of 6 new AB cell lines-generated by "conditional reprogramming"-and their genomic characterization that reveals driver mutations in FGFR2, KRAS, NRAS, BRAF, PIK3CA, and SMO. Furthermore, in proof-of-principle studies, we use the new cell lines to investigate AB oncogene dependency and drug sensitivity. Among our findings, AB cells with KRAS or NRAS mutation (MAPK pathway) are exquisitely sensitive to MEK inhibition, which propels ameloblast differentiation. AB cells with activating SMO-L412F mutation (Hedgehog pathway) are insensitive to vismodegib; however, a distinct small-molecule SMO inhibitor, BMS-833923, significantly reduces both downstream Hedgehog signaling and tumor cell viability. The novel cell line resource enables preclinical studies and promises to speed the translation of new molecularly targeted therapies for the management of ameloblastoma and related odontogenic neoplasms.

Concentration of specific amino acids at the catalytic/active centers of highly-conserved "housekeeping" enzymes of central metabolism in archaea, bacteria and Eukaryota: is there a widely conserved chemical signal of prebiotic assembly?

In alignments of 1969 protein sequences the amino acid glycine and others were found concentrated at most-conserved sites within approximately 15 A of catalytic/active centers (C/AC) of highly conserved kinases, dehydrogenases or lyases of Archaea, Bacteria and Eukaryota. Lysine and glutamic acid were concentrated at least-conserved sites furthest from their C/ACs. Logistic-regression analyses corroborated the "movement" of glycine towards and lysine away from their C/ACs: the odds of a glycine occupying a site were decreased by 19%, while the odds for a lysine were increased by 53%, for every 10 A moving away from the C/AC. Average conservation of MSA consensus sites was highest surrounding the C/AC and directly decreased in transition toward model's peripheries. Findings held with statistical confidence using sequences restricted to individual Domains or enzyme classes or to both. Our data describe variability in the rate of mutation and likelihoods for phylogenetic trees based on protein sequence data and endorse the extension of substitution models by incorporating data on conservation and distance to C/ACs rather than only using cumulative levels. The data support the view that in the most-conserved environment immediately surrounding the C/AC of taxonomically distant and highly conserved essential enzymes of central metabolism there are amino acids whose identity and degree of occupancy is similar to a proposed amino acid set and frequency associated with prebiotic evolution.

Evolutionary conservation and structural localizations suggest a physical trace of metabolism's progressive geochronological emergence.

We studied multiple sequence alignment (MSA) consensus amino acid distributional patterns in 2844 amino acid sequences of the eight enzymes of the Kreb's oxidative tricarboxylic acid pathway (oTCA) in Archaea, Bacteria and Eukarya and 5545 sequences of 33 bacteria as geochronologically separated enzymes with MSA consensus site modal identities. The 33 bacteria were 20 presumptive examples of early-oldest (Hadean-Archaean) ('Epoch I') or 13 late-newest (contemporary) ('Epoch III') appearing enzymes on Earth. The enzyme's MSA consensus sites were identified by their modal identity, % Occupancy in one of nine-graded evolutionary-conservation zones (CZs) and the Euclidean distance (Å) from each of their consensus MSA Cɑs to the same atom (Anchor-atom) in their reported functional center. These MSA consensus sites are tetrad-data points called recovered-amino acids (RAA). Across Domains, the % Occupancies of the eight-dominant RAAs of the Kreb's cycle and the 33 bacteria were found to be similarly ranked. Compared to Trifonov's 'putative ranked temporal order of the appearance of amino acids on Earth' (TOAE), the greatest statistical concordance with tetrad-RAAs across Domains were those characterized as within the most-evolutionary conserved conservation zone (CZ9), typically nearest (Å) their enzyme's catalytic/active center. The geochronologically characterized early-oldest Hadean-Archaean Bacteria 'Epoch I' enzymes, compared to late-newest Bacteria enzymes, had greater average numbers of amino acid residues/sequence and a statistically significant larger variability in their RAA compositional-Å3-volumes. The late-newest 'Epoch III' enzymes had statistically significant lower volumetric values, specifically, their native Å3-volume, void-volume and volume change on unfolding. Our enzyme data suggest a geochronological trace of 'metabolism's progressive emergence'.Communicated by Ramaswamy H. Sarma.

The greenhouse and antigreenhouse effects on Titan.

There are many parallels between the atmospheric thermal structure of the Saturnian satellite Titan and the terrestrial greenhouse effect; these parallels provide a comparison for theories of the heat balance of Earth. Titan's atmosphere has a greenhouse effect caused primarily by pressure-induced opacity of N2, CH4, and H2. H2 is a key absorber because it is primarily responsible for the absorption in the wave number 400 to 600 cm-1 "window" region of Titan's infrared spectrum. The concentration of CH4, also an important absorber, is set by the saturation vapor pressure and hence is dependent on temperature. In this respect there is a similarity between the role of H2 and CH4 on Titan and that of CO2 and H2O on Earth. Titan also has an antigreenhouse effect that results from the presence of a high-altitude haze layer that is absorbing at solar wavelengths but transparent in the thermal infrared. The antigreenhouse effect on Titan reduces the surface temperature by 9 K whereas the greenhouse effect increases it by 21 K. The net effect is that the surface temperature (94 K) is 12 K warmer than the effective temperature (82 K). If the haze layer were removed, the antigreenhouse effect would be greatly reduced, the greenhouse effect would become even stronger, and the surface temperature would rise by over 20 K.

Scatterers in Triton's Atmosphere: Implications for the Seasonal Volatile Cycle.

Nitrogen and methane ices on the surface of Triton, Neptune's largest satellite, are exchanged between the summer and winter hemispheres on a seasonal time scale. Images of the satellite's sky obtained by the Voyager 2 spacecraft show the presence of several types of scattering materials that provide insights into this seasonal cycle of volatiles. Discrete clouds, probably composed of N(2) ice particles, arise in regions of active sublimation. They are found chiefly poleward of 30 degrees S in the southern, summer hemisphere. Haze particles, probably made of hydrocarbon ices, are present above most, but not all places. Recent snowfall may have occurred at low southern latitudes in places where they are absent. The latent heat released in the formation of the discrete clouds may have a major impact on the thermal balance of the lower atmosphere. Triton may have been less red at the time of the Voyager flyby than 12 years earlier due to recent N(2) snowfall at a wide range of latitudes.

Venus: implications from microwave spectroscopy of the atmospheric content of water vapor.

From comparison of theoretical and observed microwave brightness temperatures of Venus at 1.35 centimeters, the center of a water-vapor line, we obtain an upper limit of 0.8 percent for the water-vapor mixing ratio in the lower atmosphere. This limit is consistent with the amount of water vapor detected by Venera 4, the existence of aqueous ice clouds, and a greenhouse effect caused by water vapor and carbon dioxide. The computed spectra suggest that a sensitive procedure for detection of water vapor is examination of the wavelength region between I and 1.4 centimeters.

Anthropogenic Albedo Changes and the Earth's Climate.

The human species has been altering the environment over large geographic areas since the domestication of fire, plants, and animals. The progression from hunter to farmer to technologist has increased the variety and pace more than the geographic extent of human impact on the environment. A number of regions of the earth have experienced significant climatic changes closely related in time to anthropogenic environmental changes. Plausible physical models suggest a causal connection. The magnitudes of probable anthropogenic global albedo changes over the past millennia (and particularly over the past 25 years) are estimated. The results suggest that humans have made substantial contributions to global climate changes during the past several millennia, and perhaps over the past million years; further such changes are now under way.

Implications of the gas compositional measurements of pioneer venus for the origin of planetary atmospheres.

Comparisons are made between the volatile inventories of the terrestrial planets, including Pioneer Venus data, and the predictions of three classes of theories for the origin of planetary atmospheres. Serious difficulties arise for the primary atmosphere and external source hypotheses. The grain accretion hypothesis can account for the trends in the volatile inventory from Venus to Earth to Mars, if volatiles were incorporated into planet-forming grains at nearly the same temperature for all of these planets, but at systematically lower pressures in the regions of planet formation farther from the center of the solar nebula.

Venus: estimates of the surface temperature and pressure from radio and radar measurements.

The radio brightness temperature and radar cross section spectra of Venus are in much better accord with surface boundary conditions deduced from a combination of the Mariner V results and the radar radius than those obtained by the Venera 4 space probe. The average surface temperature and pressure are approximately 750 degrees K and 90 atmospheres.

Io: an intense brightening near 5 micrometers.

Spectrophotometric observations of the jovian satellite Io on 20 and 21 February 1978 (Universal Time) were made from 1.2 to 5.4 micrometers. Io's brightness at 4.7 to 5.4 micrometers was found to be three to five times greater at an orbital phase angle of 68 degrees than at orbital phase angles of 23 degrees (5.5 hours before the brightening) and 240 degrees (20 hours after the brightening). Since the 5-micrometer albedo of Io is near unity under ordinary conditions, the observed transient phenomenon must have been the result of an emission mechanism. Although several such mechanisms were examined, the actual choice is not clear.

First results from the large probe infrared radiometer experiment.

During the descent to the surface of Venus, the large probe infrared radiometer measured the net thermal radiative flux in several spectral bandpasses. Preliminary analysis has permitted us to estimate (i) the infrared extinction coefficient profile attributable to aerosols, with respect to their visible profile, in the upper atmosphere of Venus and (ii) the water vapor mixing ratio below the clouds. An indication of the composition of a multicomponent cloud is seen in the data from the spectral bandpass from 6 to 7 micrometers.

Nuclear winter: global consequences of multple nuclear explosions.

The potential global atmospheric and climatic consequences of nuclear war are investigated using models previously developed to study the effects of volcanic eruptions. Although the results are necessarily imprecise due to wide range of possible scenaros and uncertainty in physical parameters, the most probable first-order effects are serious. Significant hemispherical attenuation of the solar radiation flux and subfreezing land temperatures may be caused by fine dust raised in high-yield nuclear surface bursts and by smoke from city and forest fires ignited by airbursts of all yields. For many simulated exchanges of several thousand megatons, in which dust and smoke are generated and encircle the earth within 1 to 2 weeks, average light levels can be reduced to a few percent of ambient and land temperatures can reach -15 degrees to -25 degrees C. The yield threshold for major optical and climatic consequences may be very low: only about 100 megatons detonated over major urban centers can create average hemispheric smoke optical depths greater than 2 for weeks and, even in summer, subfreezing land temperatures for months. In a 5000-megaton war, at northern mid-latitude sites remote from targets, radioactive fallout on time scales of days to weeks can lead to chronic mean doses of up to 50 rads from external whole-body gamma-ray exposure, with a likely equal or greater internal dose from biologically active radionuclides. Large horizontal and vertical temperature gradients caused by absorption of sunlight in smoke and dust clouds may greatly accelerate transport of particles and radioactivity from the Northern Hemisphere to the Southern Hemisphere. When combined with the prompt destruction from nuclear blast, fires, and fallout and the later enhancement of solar ultraviolet radiation due to ozone depletion, long-term exposure to cold, dark, and radioactivity could pose a serious threat to human survivors and to other species.

The dark side of Venus: near-infrared images and spectra from the Anglo-Australian observatory.

Near-infrared images and spectra of the night side of Venus taken at the Anglo-Australian Telescope during February 1990 reveal four new thermal emission windows at 1.10, 1.18, 1.27, and 1.31 micrometers, in addition to the previously discovered windows at 1.74 and 2.3 micrometers. Images of the Venus night side show similar bright and dark markings in all windows, but their contrast is much lower at short wavelengths. The 1.27-micrometers window includes a bright, high-altitude O2 airglow feature in addition to a thermal contribution from the deep atmosphere. Simulations of the 1.27- and 2.3 micrometers spectra indicate water vapor mixing ratios near 40 +/- 20 parts per million by volume between the surface and the cloud base. No large horizontal gradients in the water vapor mixing ratios were detected at these altitudes.

Jupiter: its infrared spectrum from 16 to 40 micrometers.

Spectral measurements of the thermal radiation from Jupiter in the band from 16 to 40 micrometers are analyzed under the assumption that pressure-broadened molecular hydrogen transitions are responsible for the bulk of the infrared opacity over most of this spectral interval. Both the vertical pressure-temperature profile and the molecular hydrogen mixing ratio are determined. The derived value ofthe molecular hydrogen mixing ratio, 0.89 +/- 0.11, is consistent with the solar value of 0.86.