Intersectionality and reflexivity-decolonizing methodologies for the data science process.

Using intersectionality as a methodology illuminated the shortcomings of the data science process when analyzing the viral #metoo movement and simultaneously allowed me to reflect on my role in that process. The key is to implement intersectionality to its fullest potential, to expose nuances and inequities, alter our approaches from the standard perfunctory tasks, reflect how we aid and abide by systems and structures of power, and begin to break the habit of recolonizing ourselves as data scientists.

Ethnic differences in stage of presentation of adults newly diagnosed with HIV-1 infection in south London.

OBJECTIVES: To establish whether there were ethnic differences in demographic characteristics, the stage at HIV diagnosis and reasons for and location of HIV testing between 1998 and 2000 in a large ethnically diverse HIV-1-infected clinic population in south London in the era of highly active antiretroviral therapy. METHODS: A retrospective review was carried out of all persons >18 years old attending King's College Hospital with a first positive HIV-1 test between 1 January 1998 and 31 October 2000, and of a random sample of patients attending St Thomas' hospital with a first positive HIV-1 test in the same period. Demographic data, details of reasons for and site of HIV test, clinical stage, CD4 lymphocyte count and HIV-1 viral load at HIV diagnosis were abstracted from the local database and medical records. Comparisons were made according to ethnic group (white, black African and black Caribbean) and over time (1998, 1999 and 2000). RESULTS: Of the 494 patients with new HIV-1 diagnoses between January 1998 and December 2000, 179 (36.2%) were white, 270 (54.7%) were black African and 45 (9.1%) were black Caribbean. There were significant differences across the ethnic groups in HIV risk group, reasons for and site of HIV testing, and clinical and CD4 stage at diagnosis. Among whites, 72.6% were men who had sex with men, 3.4% injecting drug users and 21.2% heterosexuals, compared to 2.2%, 0.4% and 93.3% among black Africans, and 28.9%, 0% and 68.9% among black Caribbeans (P<0.001). Black Africans were more likely to present with an AIDS diagnosis (21.3%) and a lower CD4 cell count [223 cells/microL; interquartile range (IQR) 88-348] compared to both whites (9.9%; 358 cells/microL; IQR 151-508) and black Caribbeans (17.9%; 294 cells/microL; IQR 113-380), who were intermediate between whites and black Africans in their stage of presentation. There was a statistically nonsignificant trend with time, between 1998 and 2000, towards earlier diagnosis based on the CD4 cell count in whites (323 and 403 cells/microL) and black Caribbeans (232 and 333 cells/microL), but a later diagnosis in black Africans (233 and 175 cells/microL). The majority of black Africans were HIV-tested as a result of suggestive symptoms or antenatal screening (58.4%) rather than because of perceived risk (40.5%), in contrast to the situation in whites (24.1% vs. 71.7%, respectively) or black Caribbeans (34.5% vs. 65.5%, respectively) (P<0.001). We found no significant differences across ethnic groups in age, HIV-1 viral load or year of HIV diagnosis. CONCLUSIONS: Black Africans continue to present with more advanced HIV disease than whites or black Caribbeans, with no evidence of any trend towards earlier diagnosis. Future educational campaigns designed to promote the uptake of HIV testing among black Africans and black Caribbeans will need to address the multiple barriers to testing, including misperception of risk, stigma and ready access to testing.

Reversibly bound and covalently attached ligands induce conformational changes in the omega loop, Cys69-Cys96, of mouse acetylcholinesterase.

We have used a combination of cysteine substitution mutagenesis and site-specific labeling to characterize the structural dynamics of mouse acetylcholinesterase (mAChE). Six cysteine-substituted sites of mAChE (Leu(76), Glu(81), Glu(84), Tyr(124), Ala(262), and His(287)) were labeled with the environmentally sensitive fluorophore, acrylodan, and the kinetics of substrate hydrolysis and inhibitor association were examined along with spectroscopic characteristics of the acrylodan-conjugated, cysteine-substituted enzymes. Residue 262, being well removed from the active center, appears unaffected by inhibitor binding. Following the binding of ligand, hypsochromic shifts in emission of acrylodan at residues 124 and 287, located near the perimeter of the gorge, reflect the exclusion of solvent and a hydrophobic environment created by the associated ligand. By contrast, the bathochromic shifts upon inhibitor binding seen for acrylodan conjugated to three omega loop (Omega loop) residues 76, 81, and 84 reveal that the acrylodan side chains at these positions are displaced from a hydrophobic environment and become exposed to solvent. The magnitude of fluorescence emission shift is largest at position 84 and smallest at position 76, indicating that a concerted movement of residues on the Omega loop accompanies gorge closure upon ligand binding. Acrylodan modification of substituted cysteine at position 84 reduces ligand binding and steady-state kinetic parameters between 1 and 2 orders of magnitude, but a similar substitution at position 81 only minimally alters the kinetics. Thus, combined kinetic and spectroscopic analyses provide strong evidence that conformational changes of the Omega loop accompany ligand binding.

Glucagon-like peptide 1 stimulates lipolysis in clonal pancreatic beta-cells (HIT).

Glucagon-like peptide 1 (GLP-1) is the most potent physiological incretin for insulin secretion from the pancreatic beta-cell, but its mechanism of action has not been established. It interacts with specific cell-surface receptors, generates cAMP, and thereby activates protein kinase A (PKA). Many changes in pancreatic beta-cell function have been attributed to PKA activation, but the contribution of each one to the secretory response is unknown. We show here for the first time that GLP-1 rapidly released free fatty acids (FFAs) from cellular stores, thereby lowering intracellular pH (pHi) and stimulating FFA oxidation in clonal beta-cells (HIT). Similar changes were observed with forskolin, suggesting that stimulation of lipolysis was a function of PKA activation in beta-cells. Triacsin C, which inhibits the conversion of FFAs to long-chain acyl CoA (LC-CoA), enhanced basal FFA efflux as well as GLP-1-induced acidification and efflux of FFAs from the cell. Increasing the concentration of the lipase inhibitor orlistat progressively and largely diminished the increment in secretion caused by forskolin. However, glucose-stimulated secretion was less inhibited by orlistat and only at the highest concentration tested. Because the acute addition of FFAs also increases glucose-stimulated insulin secretion, these data suggest that the incretin function of GLP-1 may involve a major role for lipolysis in cAMP-mediated potentiation of secretion.

Synthesis of fluorescent probes directed to the active site gorge of acetylcholinesterase.

Six organophosphorus compounds linked to fluorophore groups were prepared in an effort to selectively modify the active site of acetylcholinesterase and deliver probes to the gorge region. Two compounds that vary by the length of a methylene (CH2) group, pyrene-SO2NH(CH2)nNHC(O)CH2CH2P(O)(OEt)(F) (where n = 2 or 3) were found to be potent, irreversible inhibitors of recombinant mouse AChE (Ki approximately 10(5) M(-1) min(-1)). Size exclusion chromatography afforded a fluorescently-labeled cholinesterase conjugate.

Probing the active center gorge of acetylcholinesterase by fluorophores linked to substituted cysteines.

To examine the influence of individual side chains in governing rates of ligand entry into the active center gorge of acetylcholinesterase and to characterize the dynamics and immediate environment of these residues, we have conjugated reactive groups with selected charge and fluorescence characteristics to cysteines substituted by mutagenesis at specific positions on the enzyme. Insertion of side chains larger than in the native tyrosine at position 124 near the constriction point of the active site gorge confers steric hindrance to affect maximum catalytic throughput (k(cat)/K(m)) and rates of diffusional entry of trifluoroketones to the active center. Smaller groups appear not to present steric constraints to entry; however, cationic side chains selectively and markedly reduce cation ligand entry through electrostatic repulsion in the gorge. The influence of side chain modification on ligand kinetics has been correlated with spectroscopic characteristics of fluorescent side chains and their capacity to influence the binding of a peptide, fasciculin, which inhibits catalysis peripherally by sealing the mouth of the gorge. Acrylodan conjugated to cysteine was substituted for tyrosine at position 124 within the gorge, for histidine 287 on the surface adjacent to the gorge and for alanine 262 on a mobile loop distal to the gorge. The 124 position reveals the most hydrophobic environment and the largest hypsochromic shift of the emission maximum with fasciculin binding. This finding likely reflects a sandwiching of the acrylodan in the complex with the tip of fasciculin loop II. An intermediate spectral shift is found for the 287 position, consistent with partial occlusion by loops II and III of fasciculin in the complex. Spectroscopic properties of the acrylodan at the 262 position are unaltered by fasciculin addition. Hence, combined spectroscopic and kinetic analyses reveal distinguishing characteristics in various regions of acetylcholinesterase that influence ligand association.

Class A calcium channel variants in pancreatic islets and their role in insulin secretion.

The initiation of insulin release from rat islet beta cells relies, in large part, on calcium influx through dihydropyridine-sensitive (alpha1D) voltage-gated calcium channels. Components of calcium-dependent insulin secretion and whole cell calcium current, however, are resistant to L-type channel blockade, as well as to omega-conotoxin GVIA, a potent inhibitor of alpha1B channels, suggesting the expression of additional exocytotic calcium channels in the islet. We used a reverse transcription-polymerase chain reaction-based strategy to ascertain at the molecular level whether the alpha1A calcium channel isoform was also present. Results revealed two new variants of the rat brain alpha1A channel in the islet with divergence in a putative extracellular domain and in the carboxyl terminus. Using antibodies and cRNA probes specific for alpha1A channels, we found that the majority of cells in rat pancreatic islets were labeled, indicating expression of the alpha1A channels in beta cells, the predominant islet cell type. Electrophysiologic recording from isolated islet cells demonstrated that the dihydropyridine-resistant current was sensitive to the alpha1A channel blocker, omega-agatoxin IVA. This toxin also inhibited the dihydropyridine-resistant component of glucose-stimulated insulin secretion, suggesting functional overlap among calcium channel classes. These findings confirm the presence of multiple high voltage-activated calcium channels in the rat islet and implicate a physiologic role for alpha1A channels in excitation-secretion coupling in beta cells.

Anionic residue in the alpha-subunit of the nicotinic acetylcholine receptor contributing to subunit assembly and ligand binding.

To ascertain the anionic sites on the nicotinic receptor to which acetylcholine and other quaternary ammonium ligands bind, we have examined the role of an aspartyl residue (Asp-152) in the alpha-subunit. Prior photolytic labeling with agonist analogues of the neighboring residues Trp-149 and Tyr-151 suggests that their side chains reside on the binding face (also termed the (+)- or counterclockwise face) of the alpha-subunit. Asp-152 presents an anionic charge in the vicinity of these aromatic residues. Modification of the aspartate to asparagine (D152N) creates a glycosylation signal (Asn-152-Gly-Ser), and we find, on the basis of altered electrophoretic migration, that glycosylation occurs at this position upon cotransfection of the mutant alpha-subunit with beta-, gamma-, and delta-subunits. Glycosylation results in a reduction in the capacity of the receptor to assemble; this reduction is manifest in the initial step of dimer formation between the alphagamma- and alphadelta-subunits. The alpha-subunit mutant receptor reaching the assembled pentamer exhibits an altered selectivity for certain ligands. Little reduction in alpha-bungarotoxin binding is observed, whereas affinities for agonists and competitive alkaloid antagonists are reduced substantially. Separation of the contributions of charge removal and glycosylation addition shows that both factors affect agonist affinity, with the charge influence being far more predominant. These findings raise the possibility that a component of the coulombic attraction stabilizing the binding of agonists comes from the aspartyl residue at position 152 in the alpha-subunit.

Understanding, improving and using green fluorescent proteins.

Green fluorescent proteins (GFPs) are presently attracting tremendous interest as the first general method to create strong visible fluorescence by purely molecular biological means. So far, they have been used as reporters of gene expression, tracers of cell lineage, and as fusion tags to monitor protein localization within living cells. However, the GFP originally cloned from the jellyfish Aequorea victoria has several nonoptimal properties including low brightness, a significant delay between protein synthesis and fluorescence development, and complex photoisomerization. Fortunately, the protein can be re-engineered by mutagenesis to ameliorate these deficiencies and shift the excitation and emission wavelengths, creating different colors and new applications.

Clinical use of molecular information in the management of multiple endocrine neoplasia type 2A.

One hundred and ninety-seven members of 28 kindreds with multiple endocrine neoplasia type 2A (MEN 2A) were screened for RET proto-oncogene exon 10 and 11 mutations. Seventy-one known affected individuals had mutations of codons 609, 618, 620 or 634, whereas 53 unaffected individuals had no abnormalities. Nineteen out of 54 individuals of unknown status, mostly children, had RET mutations. Four of these children had thyroidectomy based on this analysis and were found to have C-cell abnormalities. We identified one false negative mutation analysis because of a codon 691 polymorphism. We conclude that RET mutational analysis is a cost-effective and accurate method for determination of gene carrier status in MEN 2A.

Cloning of the beta cell high-affinity sulfonylurea receptor: a regulator of insulin secretion.

Sulfonylureas are a class of drugs widely used to promote insulin secretion in the treatment of non-insulin-dependent diabetes mellitus. These drugs interact with the sulfonylurea receptor of pancreatic beta cells and inhibit the conductance of adenosine triphosphate (ATP)-dependent potassium (KATP) channels. Cloning of complementary DNAs for the high-affinity sulfonylurea receptor indicates that it is a member of the ATP-binding cassette or traffic ATPase superfamily with multiple membrane-spanning domains and two nucleotide binding folds. The results suggest that the sulfonylurea receptor may sense changes in ATP and ADP concentration, affect KATP channel activity, and thereby modulate insulin release.

Ligand-specificity of the rat GLP-I receptor recombinantly expressed in Chinese hamster ovary (CHO-) cells.

Glucagon-like peptide-I (GLP-I) is a potent incretin hormone and is considered as a new therapeutic tool in the treatment of diabetes mellitus. This study was designed to precisely characterize the binding behavior and activation of the recombinant GLP-I receptor against naturally occurring ligands of the glucagon/VIP/secretin peptide hormone family. CHO-cells were stably transfected with a plasmid containing a cDNA encoding for the rat GLP-I receptor. Northern blot analysis with this cDNA showed a single band of 2.7 kb in CHO cells, while in RINm5F cells, three bands of 2.7, 3.4, and 3.6 kb were specifically labelled. In receptor-binding studies 125I-GLP-I was displaced by GLP-I and weakly by PHI and oxyntomodulin but not by helodermin, helospectin I, helospectin II, secretin, VIP, and PACAP-38. Intracellular cAMP generation was stimulated by GLP-I, PHI, and oxyntomodulin. Helodermin, helospectin I, helospectin II, secretin, VIP, and PACAP-38 were not able to displace 125I-GLP-I from its receptor or to stimulate intracellular cAMP production. This data shows that the GLP-I receptor is characterized by a high ligand specificity.

Do adipocytes contain high affinity sulfonylurea receptors.

Sulfonylureas interact with specific, high affinity receptors on the pancreatic beta-cell to close ATP-sensitive K+ channels, depolarize the cell, activate Ca2+ influx through voltage-dependent Ca2+ channels, and trigger insulin secretion. We tested the hypothesis that sulfonylureas promote glucose uptake into 3T3-L1 cells or isolated rat adipocytes by similar mechanisms. Using 125I-labeled 5-iodo-2-hydroxyglyburide and either equilibrium binding or photoaffinity labeling, a high affinity sulfonylurea receptor was not found on plasma membranes of either the 3T3-L1 cells or rat adipocytes. Furthermore, glyburide did not inhibit 86Rb+ efflux (a marker for ATP-sensitive K+ channel conductance), increase free cytosolic calcium in adipocytes or 3T3-L1 cells, or increase basal or insulin-stimulated glucose uptake into 3T3-L1 cells or rat adipocytes. Parallel studies using a hamster insulin-secreting tumor cell line (HIT cells) easily demonstrated both the receptor and biological effects of glyburide on free cytosolic calcium and insulin secretion. Thus, rat adipocytes and 3T3-L1 cells do not possess the high affinity sulfonylurea receptor or respond to glyburide alone. We conclude that the antidiabetogenic effects of sulfonylureas are not mediated by a direct action of sulfonylureas to increase glucose uptake into adipose tissue and suggest that the major locus for sulfonylurea action is the beta-cell.

Management of individual tumor syndromes. Medullary thyroid carcinoma and hyperparathyroidism.

Significant advances have been made in the understanding of the pathophysiology and the ability to effectively screen for and treat medullary thyroid carcinoma. The parafollicular cells, or C-cells, are the cell of origin for medullary thyroid carcinoma. C-cell hyperplasia is a premalignant disease that progresses rapidly to medullary thyroid carcinoma. C-cells produce calcitonin, which serves as a marker to prospectively screen patients for C-cell disease. One major concern in screening for this disease has been the incidence of false positive results. This problem is addressed in light of new, more stringent criteria for the diagnosis of C-cell hyperplasia. The association of hyperparathyroidism with MEN 2 is discussed with evidence that thyroidectomy of C-cell disease may affect the incidence of parathyroid disease.

Stable expression of the rat GLP-I receptor in CHO cells: activation and binding characteristics utilizing GLP-I(7-36)-amide, oxyntomodulin, exendin-4, and exendin(9-39).

Glucagon-like peptide-I (GLP-I) is a potent insulinotropic peptide that mediates its actions at pancreatic B-cells via specific receptors. In the present study we stably expressed the rat B-cell GLP-I receptor in CHO cells and studied binding characteristics and receptor activation utilizing the naturally occurring receptor agonist GLP-I(7-36)-amide (GLP-I), the proglucagon-derived GLP-I-related peptide oxyntomodulin, the GLP-I receptor agonist exendin-4, and the specific antagonist exendin(9-39). The potencies to displace [125I]GLP-I from the receptor were GLP-I > exendin-4 > exendin(9-39) > oxyntomodulin, and to displace [125I]exendin-4 GLP-I = exendin-4 > exendin(9-39) > oxyntomodulin. cAMP production was stimulated equally by GLP-I and exendin-4. Oxyntomodulin was less potent to stimulate cAMP generation. Exendin(9-39) blocked the stimulatory action of GLP-I and exendin-4 on cAMP production, but not that of oxyntomodulin. This study shows that GLP-I and exendin-4 are potent agonists at the transfected rat B-cell GLP-I receptor whereas oxyntomodulin is only a weak GLP-I receptor agonist. Furthermore, exendin(9-39) is a potent GLP-I receptor antagonist. This peptide is a valuable tool to further study the physiological actions of GLP-I.