Nanoinformatics, and the big challenges for the science of small things.

The combination of computational chemistry and computational materials science with machine learning and artificial intelligence provides a powerful way of relating structural features of nanomaterials with functional properties. However, combining these fundamentally different scientific approaches is not as straightforward as it seems. Machine learning methods were developed for large data sets with small numbers of consistent features. Typically nanomaterials data sets are small, with high dimensionality and high variance in the feature space, and suffer from numerous destructive biases. None of the established data science or machine learning methods in widespread use today were devised with (nano)materials data sets in mind, but there are ways to overcome these challenges and use them reliably. In this review we will discuss domain-specific constraints on data-driven nanomaterials design, and explore the differences between nanomaterials simulation and nanoinformatics that can be leveraged for greater impact.

Different phenotypic consequences of simultaneous versus stepwise Apc loss.

APC is considered a gatekeeper for colorectal cancer (CRC). Cells with heterozygous APC mutations have altered expression profiles suggesting that the first APC hit may help set the stage for subsequent transformation. Therefore, we measured transformation efficiency following what we have designated as 'simultaneous' versus 'stepwise' Apc loss. We combined a conditional Apc allele (Apc(CKO)) with a Cre reporter gene and an out-of-frame Cre allele (Pms2(cre)) that stochastically becomes functional by a frameshift mutation in single cells. Loss of one Apc allele (Apc(CKO/+)) had little consequence, whereas simultaneous loss of both Apc alleles (Apc(CKO/CKO)) resulted in increased clonal expansion (crypt fission), consistent with the gatekeeper function of Apc. Interestingly, our analyses showed that most of the Apc-deficient crypts in Apc(CKO/CKO) mice appeared normal, with morphological transformation, including ß-catenin deregulation, occurring in only 17% of such crypts. To determine whether transformation efficiency was different following stepwise Apc loss, we combined Apc(CKO) with a germline mutant allele, either Apc(Min) or Apc(1638N). Transformation efficiency following stepwise Apc loss (Apc(Min/CKO) or Apc(1638N/CKO)) was increased five-fold and essentially all of the Apc-deficient cells were dysplastic. In summary, our data suggest that the gatekeeper function of Apc consists of two roles, clonal expansion and morphological transformation, because simultaneous Apc loss frequently leads to occult clonal expansion without morphological transformation, whereas stepwise Apc loss more often results in visible neoplasia. Finally, that Apc-deficient cells in certain scenarios can retain a normal phenotype is unexpected and may have clinical implications for surveillance strategies to prevent CRC.

Natural selection for grazer resistance to toxic cyanobacteria: evolution of phenotypic plasticity?

We studied the selection response of the freshwater grazing zooplankter, Daphnia galeata, to increased abundance of cyanobacteria in its environment. Cyanobacteria are a poor-quality and often toxic food. Distinct genotypes of D. galeata were hatched from diapausing eggs extracted from three time horizons in the sediments of Lake Constance, Europe, covering the period 1962 to 1997, a time of change in both the prevalence of planktonic cyanobacteria and levels of phosphorus pollution. We assessed whether the grazers evolved to become more resistant to dietary cyanobacteria by exposing genetically distinct clones to two diets, one composed only of the nutritious green alga, Scenedesmus obliquus (good food), and the other a mixture of S. obliquus and the toxic cyanobacterium Microcvstis aeruginosa (poor food). Genotype performance was measured as the specific rate of weight gain from neonate to maturity (gj). We evaluated evolutionary change in the Daphnia population using an analysis of reaction norms based on relative (log-transformed) changes in gj. Log(gj) is a measure of the proportional effect of dietary cyanobacteria on other fitness components of the Daphnia phenotype. For comparison, we also analyze absolute (i.e., nontransformed) changes in gj and discuss the interpretations of the two approaches. Statistical results using a general linear model demonstrate a significant effect of genotype (showing differences in gj among genotypes), a significant genotype x food-type interaction (showing differences in phenotypic plasticity among genotypes), and, in the case of log-transformed data, a significant sediment-genotype-age x food-type interaction. The latter shows that phenotypic plasticity evolved over the period studied. Two constraints act on response to selection in the D. galeata-Lake Constance system. First, gj on a diet containing poor food is highly correlated with gj on a diet of good food, thus evolving resistance also meant evolving an increase in gj on both diets. Second, because genotypes with a high gj also grow to a large adult body size, which in turn increases Daphnia vulnerability to fish predation, we suggest that selection only acted to favor genotypes possessing a high potential gj after cyanobacteria became prevalent. The presence of cyanobacteria depressed realized gj and led to animals of small adult body size even if their genotypes had the potential for high gj and large size. With realized gj reduced, genotypes with an inherently high value could be selected even in the presence of predatory fish. The joint action of selection by dietary cyanobacteria and vulnerability to fish predation provides an explanation for the observed evolution of resistance to poor food through reduced phenotypic plasticity.

Depletion of natural killer cells from the graft reduces interferon-gamma levels and lipopolysaccharide-induced tumor necrosis factor-alpha release in F1 hybrid mice with acute graft-versus-host disease.

BACKGROUND: We wished to determine whether removal of NK1.1+ cells from the graft provides protection against acute graft-versus-host disease (GVHD) by obviating the Th1 immune response that underlies the development of this disease. METHODS: Graft-versus-host (GVH) reactions were induced in two groups of (C57BL/6 x DBA/2)F1 hybrid mice. The first received grafts harvested from polyinosinic:polycytidylic acid-stimulated, C57BL/6 donors and depleted in vitro of NK1.1+ cells. This treatment provides protection against GVHD-associated mortality and cachexia. The second received unmodified grafts. We compared interferon-gamma and interleukin-10 production as well as the levels of engraftment in these two groups. Lipopolysaccharide-induced tumor necrosis factor-alpha (TNF-alpha) release was also compared since TNF-alpha levels in GVH mice following injection of a sublethal dose of endotoxin provide an index of macrophage priming by Th1 cytokines. RESULTS: Interferon-gamma production was absent in recipients of NK1.1-depleted grafts at the time when high levels were seen in recipients of unmodified grafts. Following lipopolysaccharide injection, high levels of TNF-alpha were observed in recipients of unmodified grafts, whereas negligible amounts were present in recipients of NK1.1-depleted grafts. The use of NK1.1-depleted grafts did not result in a reduced level of engraftment of CD4+ or CD8+ cells. CONCLUSIONS: These results suggest that NK1.1 depletion of the graft confers protection against mortality by interfering with an immunoregulatory mechanism that results in the development of a Th1 response in GVH mice, and does not result in abortion of the graft. Because macrophage priming is prevented, recipients are also protected from the exaggerated sensitivity to endotoxin seen in mice with acute GVHD.

Murine graft-versus-host disease in an F1-hybrid model using IFN-gamma gene knockout donors.

These experiments were performed to determine whether the absence of donor-derived IFN-gamma would influence the outcome of acute graft-vs-host disease (GVHD). Graft-vs-host reactions were induced in B6D2F1 hybrids using grafts from either IFN-gamma gene knockout (gko) or wild-type, C57BL/6J, parental strain donors. GVHD was equally lethal in both groups, but IFN-gamma gko graft recipients developed a more protracted form of the disease. These mice developed early wasting that persisted until death. IFN-gamma was present in spleen cell cultures from wild-type graft recipients, but was absent in cultures from IFN-gamma gko graft recipients. Both recipient groups showed macrophage priming for LPS-induced TNF-alpha release. Engraftment of donor-derived CD4+ and CD8+ cells was greater in IFN-gamma gko graft recipients. Pathologic changes in IFN-gamma gko graft recipients were different from those typically seen in acute GVHD. The syndrome developing in IFN-gamma gko recipients consisted of patchy alopecia, corneal dryness and clouding, and lymphocytic infiltration of the liver, pancreas, salivary gland, lung, and kidney. Lymphocytic infiltrates were also present in the epidermis and the epithelium of both bile and salivary gland ducts. Some of the lesions closely resembled those seen in the "sicca"/Sjogren's-like syndrome associated with chronic GVHD; however, there was no evidence of immune complex deposition in the kidney. These results indicate that GVHD in IFN-gamma gko graft recipients shares many features with acute GVHD, but both the duration of the disease and its pathologic manifestations are different. Our results suggest that IFN-gamma plays a significant role in the pathogenesis of acute GVHD by increasing the rate at which mortality develops.

Comparison of spiral CT scan and arteriography for evaluation of renal and visceral arteries.

Renal and visceral artery images obtained concurrently with spiral CT and conventional arteriography were compared for 32 patients. Indications for imaging were occlusive disease (n = 12), aneurysmal disease (n = 9), and renal or visceral artery disease (n = 11). Conventional arteriography enabled visualization of 64 renal arteries and 15 accessory renal arteries. Lateral aortograms obtained in 15 patients enabled visualization of 14 superior mesenteric (SMA) and 14 celiac arteries. Spiral CT enabled visualization of 60 renal arteries, 12 accessory renal arteries, 27 SMAs, and 22 celiac arteries. Calcification or a disparity in timing of contrast material injection and scanning prevented visualization of the celiac artery in 10 patients and the SMA in four patients. With conventional arteriography as the standard for comparison, spiral CT had a sensitivity of 67% and a specificity of 95% for depiction of at least 75% stenosis in the main renal artery. By means of the Pearson correlation coefficient, significant correlation (p < 0.001) was confirmed between spiral CT and arteriography for evaluation of stenosis of the main renal artery, SMA, and celiac artery. This early experience suggests that spiral CT may be useful in evaluation of renal and visceral arteries and their relationship to aortic disease.

Effects of forage particle size and long hay for cows fed total mixed rations based on alfalfa and corn.

A 2 x 2 factorial arrangement of treatments, in which particle length of alfalfa silage in the TMR and supplementary long alfalfa-grass hay were the factors, was used to determine whether hay benefits lactating cows and whether its effects depend on fibrosity of the main forage source. Without supplementary hay, TMR contained 45% forage, including corn silage, and 26 to 27.5% NDF. When hay was fed, the amount of alfalfa silage in the corresponding TMR was reduced. In the production trial, 40 cows (20 multiparous) were fed the diets for 8 wk in early lactation. No interactions of silage length and hay occurred on any production variables except lactose concentration in the milk of multiparous cows. Addition of hay to the diet enhanced DMI, without effect on production, so efficiency of milk production was reduced. Shorter alfalfa silage enhanced DMI by multiparous cows, reduced SCM and FCM in primiparous cows, and depressed fat test in both groups. Milk composition and component production generally were unaffected. Five rumen-fistulated cows in early to midlactation each were given the four treatments during four 3-wk periods. Hay enhanced rumination when short alfalfa silage was fed but tended to reduce it on long alfalfa silage. Hay also depressed rumen pH and enhanced VFA concentrations. Alfalfa silage length had minimal effects on rumination and no effect on fermentation, and neither hay nor silage length affected digestion of silage DM or NDF in the rumen. Addition of hay to the diet may not be beneficial for cows fed TMR, but longer term feeding studies are needed.

A murine monoclonal anti-idiotypic antibody detects a common idiotope on human, mouse and rabbit antibodies to allergen Lol p IV.

A syngeneic mouse monoclonal anti-idiotypic antibody (anti-Id), designated as B1/1, was generated against a monoclonal antibody (MoAb 91) specific for Ryegrass pollen allergen Lol p IV. This anti-Id recognized an idiotope (Id) that was also present on other monoclonal antibodies with the same specificity as MoAb 91. Observations that (i) the anti-Id inhibited the binding of MoAb 91 to Lol p IV and (ii) the Id-anti-Id interaction could be inhibited by Lol p IV indicated that the Id was located within or near the antigen combining site. These properties served to characterize B1/1 as an internal image anti-Id. Evidence that an immune response in different species to Lol p IV elicits the formation of antibodies which express a common Id was provided by the observations that (i) the Id-anti-Id interactions could be inhibited by mouse, human and rabbit antisera to Lol p IV and (ii) the binding of these antisera to Lol p IV could be inhibited by the anti-Id. Interestingly, the internal image anti-Id B1/1 also recognized an Id on a monoclonal antibody which was directed to an epitope of Lol p IV, different from that recognized by MoAb 91.

Identification of two distinct allergenic sites on ryegrass-pollen allergen, Lol p IV.

Lol p IV is an important allergen of ryegrass pollen. For the immunochemical identification of antigenic and/or allergenic site(s), murine monoclonal antibodies (MAbs) were prepared against Lol p IV. The hybridoma cell-culture supernatants were screened for anti-Lol p IV antibodies by a combination of ELISA and Western immunoblot analyses. The MAbs were finally purified from ascites on a Mono Q ion-exchange column. In a competitive radioimmunoassay with Lol p IV as the solid phase and 125I-labeled MAbs, it was established that MAbs 90, 91, 92, 93, and 94, although they differed in their relative affinities, recognized in common with one another an epitope designated as antigenic site A, whereas MAb 12 recognized a different epitope referred to as site B. Sites A and B were also demonstrated to constitute allergenic determinants of Lol p IV. Differences in the repertoire of specificities of the human IgE antibodies directed to Lol p IV were also demonstrated. Interestingly, it was found that sera from both allergic as well as from nonatopic individuals had IgG antibodies to sites A and/or B.

A new fluorescent test for cell vitality using calcofluor white M2R.

The fluorescent fabric-brightener dye, Calcofluor white M2R (CFW), can be used to distinguish between living and dead cells from a variety of animal and plant sources. CFW does not stain living mouse fibroblasts or trout red blood cells and stains only the cell walls in living cells from the epidermis of onion bulb scale, staminal hairs of Tradescantia, and longitudinal sections of broad bean stems and roots. Heat-killed plant or animal cells are recognized by their lightly stained cytoplasm and brightly stained nuclei. The optimum staining concentrations were very low (0.01% to 0.03%) and nontoxic. Using onion scale epidermis in which some cells had been killed by heating as a test system, and the plasmolysis-deplasmolysis rection as the ultimate test for cell vitality, results from CFW staining correctly predicted cell vitality for about 98% of the cells tested. This success rate was comparable to those for Evans blue, uranin or neutral red in this test system.

Mechanism of seed priming in circumventing thermodormancy in lettuce.

Lettuce (Lactuca sativa L. cv Minetto) seeds were primed in aerated solutions of 1% K(3)PO(4) or water at 15 degrees C in the dark for various periods of time to determine the manner by which seed priming bypasses thermodormancy. Seeds which were not primed did not germinate at 35 degrees C, whereas those which were primed for 20 h in 1% K(3)PO(4) or distilled H(2)O had up to 86% germination. The rate of water uptake and respiration during priming were similar regardless of soak solution. Cell elongation occurred in both water and 1% K(3)PO(4), 4 to 6 h prior to cell division. Both processes commenced sooner in water than K(3)PO(4). Radicle protrusion (germination) occurred in the priming solution at 21 h in water and 27 h in 1% K(3)PO(4).Respiration, radicle protrusion and cell division consistently occurred sooner in primed (redried) seeds compared to nonprimed seeds when they were imbibed at 25 degrees C. Cell division and elongation commenced after 10 h imbibition in primed (redried) seeds imbibed at 35 degrees C. Neither process occurred in nonprimed seeds. Respiratory rates were higher in both primed and nonprimed seeds imbibed at 35 degrees C compared to those imbibed at 25 degrees C, although radicle protrusion did not occur in nonprimed seeds which were imbibed at 35 degrees C. It is apparent that cell elongation and division are inhibited during high temperature imbibition in nonprimed lettuce seeds. Seed priming appears to lead to the irreversible initiation of cell elongation, thus overcoming thermodormancy.

Determinants of ryegrass pollen cytochrome c recognized by human IgE and murine monoclonal antibodies.

In attempts to produce fragments of an allergenic molecule which would retain allergenic and/or antigenic determinant(s), the cytochrome c of ryegrass (RG) pollen, which had been shown to be an allergenic constituent of this pollen, was digested with trypsin and chymotrypsin and the resulting fragments were separated by high performance liquid chromatography. Several of these fragments were shown, with the aid of the radioallergosorbent test and solid phase radioimmunoassays, to bind IgE antibodies present in a pool of six sera from grass-sensitive patients and three murine monoclonal antibodies, designated as Mab 41, Mab 42 and Mab 43, which had been originally produced against the crossreacting cytochrome c of Kentucky bluegrass (KBG). In summary, (i) fragments C-67 and C-74 reacted with all antibodies, (ii) fragments T-45, T-46 and C-69 bound to human IgE antibodies as well as to Mab 41 and Mab 42, but not to Mab 43, (iii) fragment T-44 reacted only with Mab 41 and Mab 42, and (iv) fragment C-83 bound only Mab 42 and Mab 43. On the basis of these results, it is concluded that (i) immunochemically active fragments of the RG cytochrome c can be readily produced by enzymatic degradation, (ii) there is significant crossreaction between the antigenic determinants of RG and KBG cytochromes c, (iii) whereas all fragments possessed at least two of the original antigenic determinants, fragments C-83 and T-44 were devoid of allergenic determinants, (iv) the antigenic determinants recognized by Mab 41 and Mab 42 were different from those reacting with human IgE antibodies and Mab 43, (v) each of the three monoclonal antibodies recognized a distinct antigenic determinant, (vi) fragments C-67 and C-74 possessed all determinants recognized by the human IgE and mouse antibodies used.

Regional measurements of blood flow in experimental RG-2 rat gliomas.

Regional measurements of blood flow (F) were performed in transplanted intracerebral RG-2 rat gliomas using [14C]iodoantipyrine, Kety-Schmidt blood flow equations, and quantitative autoradiography. Twenty-nine intracranial tumors in ten rats were analyzed by location; 18 intraparenchymal, seven meningeal, two third-ventricular, and two fourth-ventricular tumors were studied. For all tumors, averaged mean F was 91 +/- 33 (S.D.) ml/hg/min. In all but one tumor, mean F was intermediate between normal cortex and corpus callosum values. There was moderate regional variation: averaged mean F was lower in tumor center (78 +/- 47 ml/hg/min) than in tumor periphery (93 +/- 30 ml/hg/min). Within individual tumors, F showed moderate variation which correlated to some extent with histological features; a regional F of less than 10 ml/hg/min was observed in only one tumor within an area of necrosis. F in regions of brain immediately surrounding the tumor was higher than in tumor periphery. Blood flow to RG-2 tumors seems unlikely to limit drug delivery any more than to normal brain, and the consistent levels from tumor to tumor and within individual tumors make the RG-2 model an excellent one with which to study drug delivery in experimental brain tumors.

Regional measurements of blood-to-tissue transport in experimental RG-2 rat gliomas.

Regional measurements of blood-to-tissue transport were performed in transplanted RG-2 rat gliomas using [alpha- 14C]aminoisobutyric acid (AIB), quantitative autoradiography, and equations to express a unidirectional transfer constant. Thirty-eight intracranial tumors in ten rats were analyzed according to location; 23 intraparenchymal tumors, eight meningeal tumors, six fourth-ventricular tumors, and one third-ventricular tumor were studied. Except for the small third-ventricular tumor, the transfer constant (K) for AIB was similar in all groups and ranged from 0.031 to 0.038 ml/g/min. Within individual tumors, regional variation of K was also small, although some local variation could be correlated with histological features. The K for AIB decreased in brain around tumor and, at a distance of 300 microns from tumor edge, had returned to values similar to those of normal cortex (0.002 ml/g/min). An average extraction fraction (E) of 0.09 was calculated for AIB in the RG-2 tumors. The low E suggests that delivery of water-soluble chemotherapeutic drugs to RG-2 tumors should be limited more by capillary permeability or surface area than by blood flow. RG-2 is an ideal experimental tumor with which to test drug delivery and the methods that attempt to increase drug delivery in brain tumors.

Regional cerebral blood flow in the beagle puppy model of neonatal intraventricular hemorrhage: studies during systemic hypertension.

The newborn beagle puppy serves as an animal model for intraventricular hemorrhage (IVH) of the premature infant. Since increased systemic blood pressure has been implicated in the genesis of IVH in both babies and puppies, we studied regional cerebral blood flow in control and hypertensive puppies. Hypertension significantly increased blood flow to all structures. The largest increases occurred in gray matter, especially deep cerebral and brainstem nuclei. Blood flow also increased to deep hemispheric white matter, but the magnitude of the increase was smaller. Hypertension also increased blood flow to the subependymal germinal matrix (GM). The magnitude of the increase to most of the GM was small and similar to deep hemispheric white matter. The increase to the most rostral GM was higher and equal to the mean increase seen in gray matter. This rostral-caudal gradient of hypertension-induced hyperperfusion may explain the tendency for IVH to occur in rostral GM in premature babies. However, the failure to find a disproportionate increase in blood flow to GM during hypertension implies that additional factors besides hypertension-induced GM hyperperfusion may be involved in the pathogenesis of IVH.

Spatial distribution of proliferating cells in avian sarcoma virus-induced gliomas.

We studied the regional distribution of proliferating tumor cells in five avian sarcoma virus-induced gliomas. The labeling index and spatial distribution of [3H]thymidine (dThd)-labeled tumor cells were determined in serial sections of each tumor with a computer-assisted digitizing system. The density of [3H]dThd-labeled cells showed marked regional variation in each tumor, and the ratio of the density of [3H]dThd-labeled cells in tumor periphery to tumor center varied from 0.86 to 1.38. The labeling index generally, but not always, reflected [3H]dThd-labeled cell density. This study indicates that proliferating pools of glioma tumor cells exhibit regional variability in concentration and that the highest numbers of proliferating cells may be predominantly located in central regions of tumor and not in tumor periphery as assumed previously. In all tumors, large numbers of proliferating cells were present in all parts of the tumor.

Regional cerebral blood flow in the newborn beagle pup: the germinal matrix is a "low-flow" structure.

The newborn beagle pup serves as a model for neonatal intraventricular hemorrhage (IVH). Fluctuations in germinal matrix blood flow are left to play a major role in the pathogenesis of IVH. We studied regional cerebral blood flow in awake newborn beagle pups utilizing [14C]-iodoantipyrine as a blood flow indicator and quantitative autoradiography. The equilibrium [tissue]:[blood] partition coefficient for iodoantipyrine was 1.13 +/- .06 for grey matter. Blood flow was calculated for cerebral cortex (frontal = 59 +/- 9 ml/100 g/min), 14 subcortical nuclear structures (e.g., caudate = 45 +/- 6 ml/100 g/min), 3 white matter structure (centrum semiovale = 7 +/- 1 ml/100 g/min), and germinal matrix (7 +/- 1 ml/100 g/min) (mean +/- S.E.). We conclude that under normal physiologic conditions the germinal matrix receives relatively low blood flow. This information can be used for comparison with germinal matrix blood flow during adverse experimental conditions.

Permeability of different experimental brain tumor models to horseradish peroxidase.

The permeability of different brain tumor models to horseradish peroxidase (HRP) was examined by determining the fraction of tumor that contained HRP after intravenous administration. The intracerebral tumor models studied were Avian Sarcoma Virus (ASV)-induced tumors and tumors from transplanted RG-2, S69-C1-5, and 9L cell lines. The average fraction of RG-2 tumors permeable to HRP was .95; of S69-C1-5 tumors, .699; of ASV-induced tumors. .63; and of 9L tumors, .52. Except for the RG-2 tumors, there was considerable regional variation in HRP permeability, which was most marked in the ASV-induced tumors. In ASV-induced tumors, HRP permeability did not correlate with tumor histological classification, size, or anatomic location within the brain. The subcutaneous tumor models studied were RG-2-, S69-C1-5, and 9L-transplanted tumors in rats, and human glioblastoma cell lines transplanted into nude mice. All were completely permeable to HRP. These results indicate that significant differences in permeability to HRP exist among brain tumor models when the tumors are intracerebral, and that all subcutaneous tumors from transplanted glial cell lines are completely permeable to HRP. These variables must be considered in future studies of permeability in experimental brain tumors. Care must be exercised in extrapolating results about permeability from one brain tumor model to another.