A guide to the BRAIN Initiative Cell Census Network data ecosystem

Characterizing cellular diversity at different levels of biological organization and across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also essential to manipulate cell types in controlled ways and to understand their variation and vulnerability in brain disorders. The BRAIN Initiative Cell Census Network (BICCN) is an integrated network of data-generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate (NHP) brains. Here, we provide a guide to the cellular and spatial approaches employed by the BICCN, and to accessing and using these data and extensive resources, including the BRAIN Cell Data Center (BCDC), which serves to manage and integrate data across the ecosystem. We illustrate the power of the BICCN data ecosystem through vignettes highlighting several BICCN analysis and visualization tools. Finally, we present emerging standards that have been developed or adopted toward Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience. The combined BICCN ecosystem provides a comprehensive resource for the exploration and analysis of cell types in the brain.

Lateral habenula integration of proactive and retroactive information mediates behavioral flexibility

The lateral habenula (LHb) is known to play an important role in signaling aversive or adverse events that have happened or are predicted by cues under Pavlovian conditions. In rodents, it is also required for behavioral flexibility when changes in reward outcomes signal that strategies should be changed. It is not known whether the LHb also controls appetitive behaviors when an animal is able to utilize external cues proactively to guide upcoming decisions. In order to test this, male Long-Evans rats were trained to switch between two arms of a figure eight maze based on the tone presented prior to the choice. Importantly, the tones were switched every three to six trials so rats were able establish a response pattern before being required to switch. This caused rats to rely on both proactive (tones) and retroactive information (reward feedback) to guide behavior. Inactivation of the LHb with the GABA agonists baclofen and muscimol impaired overall performance by increasing both errors when the tones are switched (switch errors) as well as on subsequent trials (perseverative errors) indicating that both proactive and retroactive information are utilized by the LHb to guide behavioral flexibility. Once a correct choice was made in a given block, LHb inactivated rats did not make more errors than controls. A control study revealed that the LHb is not required for tone or reward magnitude discrimination per se. These results demonstrate for the first time that the LHb contributes to behavioral flexibility through utilizing both proactive and retroactive information when performing appetitive tasks.

Monocyte activity is linked with abdominal aortic aneurysm diameter

BACKGROUND

Systemic inflammation and increased matrix metalloproteinase (MMP) cause elastin degradation leading to abdominal aortic aneurysm (AAA) expansion. Several prospective studies report that statin therapy can reduce AAA expansion through anti-inflammation. We hypothesize that monocyte activity plays a pivotal role in this AAA development and this study examines patient peripheral blood monocyte cell adhesion, transendothelial migration, and MMP concentrations between AAA and non-AAA patients.

MATERIALS AND METHODS

Peripheral blood was collected and monocytes isolated from control (n=15) and AAA (n=13) patients. Monocyte adhesion, transmigration, and permeability assays were assessed. Luminex assays determined MMP-9 and tissue inhibitor of metalloproteinase-4 (TIMP-4) concentrations from cell culture supernatant and patient serum.

RESULTS

AAA patient monocytes showed increased adhesion to the endothelium relative fluorescence units (RFU, 0.33±0.17) versus controls (RFU, 0.13±0.04; P=0.005). Monocyte transmigration was also increased in AAA patients (RFU, 0.33±0.11) compared with controls (RFU, 0.25±0.04, P=0.01). Greater numbers of adhesive (R2=0.66) and transmigratory (R2=0.86) monocytes were directly proportional to the AAA diameter. Significantly higher serum levels of MMP-9 (2149.14±947 pg/mL) were found in AAA patients compared with controls (1189.2±293; P=0.01). TIMP-4 concentrations were significantly lower in AAA patients (826.7±100 pg/mL) compared with controls (1233±222 pg/mL; P=0.02). Cell culture supernatant concentrations of MMP and TIMP from cocultures were higher than monocyte-only cultures.

CONCLUSIONS

Monocytes from AAA patients have greater adhesion and transmigration through the endothelium in vitro, leading to elevated MMP-9 levels and the appropriate decrease in TIMP-4 levels. The ability to modulate monocyte activity may lead to novel medical therapies to decrease AAA expansion.

Localized DNA cleavage secondary to genotoxic exposure adjacent to an Alu inverted repeat

Radiation is a potent inducer of DNA damage leading to both random DNA loss and mutation. As part of a study focused on the mechanism whereby cells undergo loss of heterozygosity (LOH), a region of common LOH telomeric termination at 11q24 was observed in clones of H292 mucoepidermoid cells established after irradiation (IR). A 10-kbp region including the telomeric extent of LOH termination was analyzed after IR using six sets of ligation-mediated polymerase chain reaction (PCR) primers to detect the presence of DNA breaks. A cluster of DNA breaks was detected that closely mapped to the telomeric extent of LOH and which were observed up to 8 hr after IR. Repeating the experiment in the presence of the inhibitor of apoptosis, zVAD.fmk, did not change the location or amount of cleavage. A similar distribution of breaks was also seen in the MCF-10A breast cancer cell line after IR. Further inspection of the involved region showed that 22/32 and 7/7 DNA breaks found in H292 and MCF-10A cells, respectively, were located either in or immediately adjacent to an AluSx1 sequence, itself ≈ 1 kbp 5' to an AluSq2 that was in an inverted orientation to the AluSx1. The region between the inverted Alu repeats was notable for both DNAse hypersensitivity and an open chromatin conformation inferred from histone modification data. These factors may contribute to genomic instability at this location.

Abstract 3888: Ionizing radiation destabilizes inverted ALU repeats linked to LOH

Ionizing radiation is a potent inducer of Loss of Heterozygosity (LOH), driven primarily by DNA double strand breaks. Such a process impacts both tumorigenesis through deletion of linked tumor suppressor genes and, similarly, the potential development of radiation resistant tumor clones during radiation therapy. The human mucoepidermoid cell line, H292, was exposed to either 4 or 8 Gy and surviving clones developed from two rounds of cloning analyzed for LOH using polymorphic microsatellite markers. A high level of LOH was observed within individual clones extending from 11q21 to 11q24 (6/49 after 4 Gy and 8/50 after 8Gy). More detailed analysis using a SNP screen on selected LOH positive clones indicated a sharp telomeric termination of LOH adjacent to a common SNP location. The telomeric extent of LOH observed co-mapped to a region of elevated recombination instability documented previously using linkage analysis. Further, SNP analysis showed a region of approximately 1 Mbp LOH that included the region of recombination instability identified through linkage analysis, in some clones isolated either with or without irradiation. The consistency of the telomeric boundary of LOH observed in the irradiated clones permitted a targeted analysis of DNA double strand breaks at this location, using LM-PCR, both before and after 4Gy irradiation of the same cell line. Using a six primer set screen covering a 9 kbp region at the telomeric extent of radiation-induced LOH, a single primer set showed an elevation in DNA breaks from 2-8h after irradiation. The timing and discrete distribution of such breaks indicated that these were not directly induced by the radiation itself. Cells that were unirradiated were not affected. Further inspection of the location demonstrating selective radiation-linked fragmentation showed the presence of an ALU inverted repeat, separated by approximately 1kbp, where the DNA breaks determined by LM-PCR were clustered within the 5’ ALU. Others have shown previously that inverted ALU repeats separated by <20bp are recombinationally unstable and are underrepresented within the human genome. It is proposed that, within the H292 cell line, otherwise stable ALU inverted repeats are capable of forming a transient hairpin conformation, perhaps facilitated by their own transcription via RNA polymerase III, which is unstable within a genome undergoing DNA damage and repair. The combination of such inverted ALU repeats and genotoxic exposure, such as during radiation therapy, may therefore destabilize specific regions of the genome and contribute to the development of aberrant cell clones.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3888. doi:10.1158/1538-7445.AM2011-3888

11q21.1-11q23.3 Is a site of intrinsic genomic instability triggered by irradiation

The chromosome location, 11q21-23, is linked to loss of heterozygosity (LOH) in multiple tumors including those of breast, lung, and head and neck. To examine the process of LOH induction, the H292 cell line (human muco-epidermoid carcinoma) was irradiated or treated with anti-CD95 antibody, and individual clones isolated through two rounds of cloning. Regions of LOH were determined by screening a suite of eight polymorphic microsatellite markers covering 11p15-11q24 using fluorescent primers and genetic analyzer peak discrimination. LOH induction was observed extending through 11q21.1-11q23.3 in 6/49 of clones surviving 4 Gy and 8/50 after 8 Gy. Analysis of selected clones by Affymetrix 6.0 single nucleotide polymorphism (SNP) arrays confirmed the initial assessment indicating a consistent 27.3-27.7 Mbp deletion in multiple clones. The telomeric border of LOH mapped to a 1 Mbp region of elevated recombination. Whole genome analysis of SNP data indicated that site-restricted LOH also occurred across multiple additional genomic locations. These data indicate that 11q21.1-11q23.3, and potentially other regions of this cell line are sites of intrinsic cell-specific instability leading to LOH after irradiation. Such deletions may subsequently be propagated by genetic selection and clonal expansion.

Disruption of coherent oscillations in inhibitory networks with anesthetics: role of GABA(A) receptor desensitization

The effect of anesthetic drugs at central synapses can be described quantitatively by developing kinetic models of ligand-gated ion channels. Experiments have shown that the hypnotic propofol and the sedative benzodiazepine midazolam have similar effects on single inhibitory postsynaptic potentials (IPSPs) but very different effects on slow desensitization that are not revealed by examining single responses. Synchronous oscillatory activity in networks of interneurons connected by inhibitory synapses has been implicated in many hippocampal functions, and differences in the kinetics of the GABAergic response observed with anesthetics can affect this activity. Thus we have examined the effect of propofol and midazolam-enhanced IPSPs using mathematical models of self-inhibited one- and two-cell inhibitory networks. A detailed kinetic model of the GABA(A) channel incorporating receptor desensitization is used at synapses in our models. The most dramatic effect of propofol is the modulation of slow desensitization. This is only revealed when the network is driven at frequencies that are thought to be relevant to cognitive tasks performed in the hippocampus. The level of desensitization at synapses with propofol is significantly reduced compared to control synapses. In contrast, midazolam increases macroscopic desensitization at network synapses by altering receptor affinity without concurrently modifying desensitization rates. These differences in gating between the two drugs are shown to alter network activity in stereotypically different ways. Specifically, propofol dramatically increases the amount of excitatory drive necessary for synchronized behavior relative to control, which is not the case for midazolam. Moreover, the range of parameters for which synchrony occurs is larger for propofol but smaller for midazolam, relative to control. This is an important first step in linking alterations in channel kinetics with behavioral changes.

Ovarian mucinous carcinoids including some with a carcinomatous component: a report of 17 cases

Only rare primary mucinous (goblet cell) carcinoids of the ovary have been reported, and their clinicopathologic features have not been well delineated. The authors studied 17 examples from patients 14 to 74 years of age. The clinical presentations were similar to those of ovarian neoplasms in general. The tumors ranged from 0.8 to 30 cm in diameter. In six cases the tumor was in the wall of a mature cystic teratoma, appearing grossly as solid nodules or areas of thickening in four of them, six tumors were entirely solid, and five were solid associated with other types of cystic tumor. The tumors were divided into three groups on the basis of their microscopic features. Six neoplasms, designated "well differentiated," were composed of small glands, many of which floated in pools of mucin. The glands were lined by goblet cells and columnar cells, some of which were of neuroendocrine type. Three tumors, designated "atypical," were characterized by crowded glands, some of which were confluent, small islands with a cribriform pattern, and scattered microcystic glands. The glands were lined by cuboidal to columnar cells, some of them neuroendocrine, admixed with goblet cells. Eight tumors, designated "carcinoma arising in mucinous carcinoid," contained islands and larger nodules of tumor cells, or closely packed glands, as well as single cells, mainly of the signet ring cell type. Most of the cells were devoid of mucin and were severely atypical with marked mitotic activity. Necrosis was present in all eight tumors. Seven of the eight tumors with a carcinomatous component contained at least minor foci of well-differentiated mucinous carcinoid; the eighth contained only foci of atypical mucinous carcinoid. The neuroendocrine nature of a variable proportion of the cells in all three groups was demonstrated by staining for neuroendocrine markers. The mucinous nature of other cells was confirmed by mucicarmine or Alcian blue stains. The ovary contained an intrinsic component of trabecular and insular carcinoid, and of strumal carcinoid in one case each, an adjacent mature cystic teratoma in six cases, mucinous cystadenocarcinoma in three cases, and borderline mucinous cystic tumor, borderline Brenner tumor, and epidermoid cyst in one case each. Fifteen tumors were stage I, one was stage II, and one was stage III. The last two tumors had a carcinomatous component. Follow-up data were available for 15 patients; 12 were alive and free of tumor 2.3 to 14 years (average, 4.7 years) after the ovarian tumor was excised. One patient, whose tumor had a carcinomatous component, died 3 years postoperatively of unrelated causes. Two patients, both of whom had a carcinomatous component in their tumor, died 9 and 12 months postoperatively. Primary mucinous carcinoids must be distinguished from metastatic mucinous carcinoid tumors from the appendix or elsewhere. Features supporting an ovarian origin are the additional presence in the specimen of teratoma or an ovarian surface epithelial tumor, an absence of blood vessel or lymphatic space invasion, and confinement to a single ovary. Similar features help to distinguish mucinous carcinoids from Krukenberg tumors. Mucinous carcinoids should also be distinguished from strumal carcinoids, which can contain mucinous glands, and insular carcinoid tumors that arise rarely in the wall of a mucinous cystic neoplasm. Although the number of cases in this series is small, the follow-up data suggest that the degree of differentiation, particularly the presence of frank carcinoma, is an important prognostic factor.

Radiation-induced pseudocarcinomatous proliferations of the urinary bladder: a report of 4 cases

Four cases of radiation cystitis that caused diagnostic difficulty because of an epithelial proliferation with architectural complexity and reactive cytologic atypia are described. The patients, 2 male, 2 female, were from 43 to 77 years of age. Two presented with hematuria. Cystoscopy disclosed abnormalities in 3 patients. Microscopic examination showed irregularly shaped and arranged aggregates of epithelial cells in the upper and mid zones of the lamina propria. The cells, which typically showed at least mild, and sometimes severe, pleomorphism, were usually transitional, but squamous differentiation was seen focally in 3 cases. Ulceration of the overlying epithelium was present in all cases and was prominent and associated with conspicuous fibrin and hemorrhage in one of them. Edema of the lamina propria was present in 3 cases, whereas lamina propria fibrosis and chronic inflammation were present in all cases. The presence in all 4 cases of vascular ectasia and other changes characteristic of radiation injury, such as atypical fibroblasts, prompted investigation of the clinical history in 2 cases in which the pathologist was unaware that the patient had received radiation. Pseudocarcinomatous proliferations in the bladder caused by radiation injury have received limited attention in the literature. Our cases illustrate the potential diagnostic errors with which these lesions may be associated.

Superficial endometriosis of the uterine cervix: a report of 20 cases of a process that may be confused with endocervical glandular dysplasia or adenocarcinoma in situ

Twenty cases of superficial endometriosis of the uterine cervix that occurred in patients from 20 to 51 (mean 37.1) years of age are described. The majority of the cases were seen in consultation and were usually referred because of diagnostic problems; endocervical glandular dysplasia, adenocarcinoma in situ, or rarely invasive adenocarcinoma were a frequent consideration of the contributor. The endometriosis was almost always an incidental microscopic finding. The endometriotic foci were usually confined to the superficial third of the cervical wall, but in one case there was also involvement of the middle third of the cervical wall. Deep cervical endometriosis was not present in any case. The endometriotic glands were typically evenly spaced and were surrounded at least focally by endometriotic stroma in all cases. The endometriotic stromal cells, however, were significantly obscured by inflammatory cells (two cases), inflammatory cells and hemorrhage (two cases), hemorrhage (four cases), and in one case by smooth muscle metaplasia causing initial failure to recognize the stromal component of the process. The presence of mitotic figures in the glandular epithelium contributed to an initial diagnosis of a premalignant or malignant glandular lesion being made or seriously entertained in 10 cases. Awareness that mitotic figures may be conspicuous in endometriosis from women of reproductive age, the usually bland cytologic features of the endometriotic epithelium, and the presence of associated endometrial stromal cells all facilitate establishing the correct diagnosis.

Identification of Mutations in the Human Factor VII Gene

It has been recognized from the early 1800s that activation of coagulation can be initiated by the exposure of subendothelial layers (tissue factor), but it was the 1940s before factor VII (FVII) was included in this event (1,2). The discovery of hemophilia A and B supported the hypothesis that the intrinsic pathway incorporating factors VIII and IX was more important in hemostasis (3,4). More recently the extrinsic pathway (incorporating FVII) has been the focus of attention by activating both arms of the coagulation cascade via its action upon factors IX and X (5).

The status of age: preliminary results

This study tested the hypothesis that there is an inverted U curve of status or prestige across the lifespan in Western culture. Although several theorists have suggested that young and old persons are accorded less status than the middle-aged, almost no empirical evidence exists on this subject. The factorial survey method was used to measure perceptions of the status of ages 5 to 100 for men and women. A set of 28 age by sex profiles were rated by 334 students. Ratings were made on a 7-point category scale. The data fit the theoretical predictions extremely well, with one notable exception. Very high ratings were given to 100-year-old people by almost half of the respondents. This anomaly was probably due to the rarity of centenarians.

New bacteriophage typing system for Yersinia enterocolitica, Yersinia kristensenii, Yersinia frederiksenii, and Yersinia intermedia: correlation with serotyping, biotyping, and antibiotic susceptibility

Yersinia enterocolitica is listed as a single species in Bergey's Manual of Determinative Bacteriology, but has recently been split into "true" Y. enterocolitica, Y. kristensenii, Y. intermedia, and Y. frederiksenii. From 48 bacteriophages isolated from raw sewage, 24 were chosen as being the most useful for differentiating strains within the four Yersinia species. The composite set of 24 phages typed 92% of 236 Y. enterocolitica strains, 100% of 16 Y. kristensenii strains, 97% of 29 Y. frederiksenii strains, and 90% of 20 Y. intermedia strains. The most common phage type in any of the groups contained 22% of the strains tested, but most of the phage types contained greater than 5% of the strains. The new typing schema was tested in three outbreaks of Y. enterocolitica, and the results agreed well with serotyping and epidemiological findings. In the same outbreaks, biotyping (API 20E profiles; Analytab Products, Plainview, N.Y.) and antibiograms were less reliable markers and probably should be used only in conjunction with serotyping or phage typing or both. Caution should be used in identifying cultures of Y. frederiksenii and Y. intermedia with the API 20E system, since the tests at 37 degrees C for L-rhamnose and melibiose fermentation are often delayed past 24 h, which is the cut-off point for the final reading in the API system. There were distinct differences in the susceptibilities of Y. enterocolitica and Y. kristensenii to ampicillin, carbenicillin, and cephalothin, which adds further support for classifying the latter as a separate species.

Drug-induced depression and attempted suicide

Sixty-eight patients who had attempted suicide were matched with non-suicidal patients with similar diagnoses to assess the extent to which excessive drug ingestion by the suicidal group might have contributed to their behaviour. It was found that the suicidal patients were consuming more drugs, particularly those of a potentially depressing kind. The implications of this finding are discussed.

Smoking and other factors affecting the conservative management of peripheral vascular disease

Three hundred and ninety patients with peripheral vascular disease, who were neither eligible for, nor fit to undergo, surgery, have been studied in a prospective trial to assess the effectiveness of adequate active conservative therapy. These patients were followed up from 4 to 72 months, the duration of the average follow-up being 24 months. There was a 72% over-all improvement rate. The most striking feature of the trial was the correlation between smoking and failure to improve.

The use of mortality data in setting priorities for disease prevention

The examination of specific disease mortality by five-year age groups helps identify health problems as problems of people and how they live. Traditional methods of examining data in broad classifications tend to obscure etiological factors and the importance of behaviour. Violence, a major cause of death in young adults, gives way to so-called diseases of indulgence in middle age, especially among men who have a much higher death rate than women. Male life expectancy at age 40 has increased only marginally in the past 40 years. Health-related human behaviour must be considered within an ecological framework since social, cultural and physical environmental differences as well as personal factors influence life-style. The responsibility for prevention rests more with the individual and society at large than with health workers. Probability tables, Health Hazard Appraisal (a system of personal risk assessment) and personal counselling can reinforce healthful life-styles and help correct hazardous ones.

Chemoprophylactic agents in schistosomiasis: eremanthine, costunolide, -cyclocostunolide and bisabolol

The wood oils of the trees Eremanthus elaeagnus Sch.-Bip., Vanillosmopsis erythropappa Sch.-Bip. and Moquinea velutina Bong. inhibit penetration of cercariae of the trematode Schistosoma mansoni. The effect is due to the presence of α,β-unsaturated sesquiterpene lactones of which three, eremanthine (I), costunolide (III) and α-cyclocostunolide (V), have been characterized. The sesquiterpene alcohol (-)-bisabolol (II) present in two of the oils is weakly active while dihydro-β-cyclocostunolide (VI) which lacks the unsaturated lactone function is inactive. I and V react with the sulphydryl group of cysteine, and their activity may be related to inhibition of sulphydryl groups in cercarial enzymes.

Summary of a Canadian study of smoking and health

The object of this study was to investigate the relationship between residence, occupation and smoking habits, and mortality from chronic diseases, particularly lung cancer. It was a prospective study, initiated by a questionnaire sent to Canadian veteran pension recipients. The study was based on the replies of 78,000 males and 14,000 females, together with data on the deaths occurring among these respondents over a six-year follow-up period-July 1, 1956 to January 30, 1962.The outstanding finding of this study was that cigarette smokers compared to non-smokers had excessive mortality, particularly from heart and circulatory diseases, lung cancer, and bronchitis and emphysema. The mortality ratios for heart and circulatory diseases were elevated even for those who smoked cigarettes less than five years, and remained relatively constant as the duration of smoking increased. The mortality ratios for lung cancer increased markedly as the duration of smoking increased. A small excess in mortality was noted among urban residents. An association between cause of death and occupation was not evident in this study.Findings based on the data on smoking collected in this study were incorporated into the Report of the U.S. Surgeon-General's Advisory Committee on Smoking and Health.