Miracle-dz/UniFAR-FTUs huggingface dataset:
Affinity Tag Coating Enables Reliable Detection of Antigen-Specific B Cells in Immunospot Assays

Assessment of humoral immunity to SARS-CoV-2 and other infectious agents is typically restricted to detecting antigen-specific antibody in the serum. Rarely does immune monitoring entail assessment of the memory B cell compartment itself, although it is these cells that engage in secondary antibody responses capable of mediating immune protection when pre-existing antibodies fail to prevent re-infection. There are few techniques that are capable of detecting rare antigen-specific B cells while also providing information regarding their precursory frequency, class/subclass usage and functional affinity. In theory, the ELISPOT/FluoroSpot (collectively ImmunoSpot) assay platform is ideally-suited for antigen-specific B cell assessments since it provides this information at single-cell resolution for individual antibody-secreting cells (ASC). Here, we tested the hypothesis that antigen coating efficiency could be universally improved across a diverse set of viral antigens if the standard direct (non-specific, low affinity) antigen absorption to the membrane was substituted by high affinity capture. Specifically, we report an enhancement in assay sensitivity and a reduction in required protein concentrations through the capture of recombinant proteins via their encoded hexahistidine (6XHis) affinity tag. Affinity tag antigen coating enabled detection of SARS-CoV-2 Spike receptor binding domain (RBD)-reactive ASC, and also significantly improved assay performance using additional control antigens. Collectively, establishment of a universal antigen coating approach streamlines characterization of the memory B cell compartment after SARS-CoV-2 infection or COVID-19 vaccinations, and facilitates high-throughput immune monitoring efforts of large donor cohorts in general.
PII: S0925-4773(99)00056-8

In Xenopus, three neural-speci®c elav-like genes (ELGs) have been identi®ed, elrB/Xel-1, elrC and elrD. With the aim to highlight possible differences in the regulation of these genes, we compared their expression patterns during development. We had previously shown that elrB is expressed from the early tailbud stage onwards, in both the central and peripheral nervous system. Here we show that both elrC and elrD are expressed earlier than elrB in the developing neural tube and the cranial ganglia, with different temporal speci®cities. Double in situ hybridizations on brain cross-sections allowed us to de®ne precisely the expression domains of elrB, elrC and elrD in the brain at the tailbud stage. What emerges from this study is a differential distribution of ELGs transcripts in the hindbrain. Also, double labeling with a motor neuron marker shows that in stage 41 tailbud embryos, elrD remains strongly expressed in motor neurons whereas elrC is mostly expressed in non-motor neuron cells. q 1999 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(01)00311-2

We describe the cloning and the expression pattern of insulin promoter factor 1 in the ascidian Ciona intestinalis (Ci-IPF1). Northern blot analysis showed that transcripts appeared at the late tailbud stage and increased at the larval stage. We have raised a speci®c antibody against the Ci-IPF1-GST fusion protein to determine the spatial expression of this gene. The protein is immunodetected at the larval stage in the sensory vesicle, in the visceral ganglion and in the mesenchymal cells. Our results support the hypothesis that IPF1/IDX1 might have extrapancreatic functions during animal development, particularly in neural cells. q 2001 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(00)00523-2

We report the identi®cation of a fourth member of the VPS10 domain containing receptor family, SorCS2, highly expressed in the developing and mature murine central nervous system. During early central nervous system development its main site of expression is the ̄oor plate. In addition, high transcript levels were detected transiently in a variety of brain regions including the dopaminergic midbrain nuclei and the dorsal thalamus. Outside the nervous system expression is detected in lung and heart and transiently in a variety of mesodermally derived tissues. q 2001 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(99)00157-4

Decapentaplegic (Dpp) signaling determines the number of cells that migrate dorsally to form the dorsal primary branch during tracheal development. We report that Dpp signaling is also required for the differentiation of one of three different cell types in the dorsal branches, the fusion cell. In Mad mutant embryos or in embryos expressing dominant negative constructs of the two type I Dpp receptors in the trachea the number of cells expressing fusion cell-speci®c marker genes is reduced and fusion of the dorsal branches is defective. Ectopic expression of Dpp or the activated form of the Dpp receptor Tkv in all tracheal cells induces ectopic fusions of the tracheal lumen and ectopic expression of fusion gene markers in all tracheal branches. Among the fusion marker genes that are activated in the trachea in response to ectopic Dpp signaling is Delta. In conditional Notch loss of function mutants additional tracheal cells adopt the fusion cell fate and ectopic expression of an activated form of the Notch receptor in fusion cells results in suppression of fusion cell markers and disruption of the branch fusion. The number of cells that express the fusion cell markers in response to ectopic Dpp signaling is increased in Notch mutants, suggesting that the two signaling pathways have opposing effects in the selection of the fusion cells in the dorsal branches. q 1999 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0042-6989(00)00110-3

We investigated human sensitivity to vertical mirror symmetry in noise patterns filtered for narrow bands of variable orientations. Sensitivity is defined here as the amount of spatial phase randomization corresponding to 75% correct performance in a 2AFC detection task. In Experiment 1, sensitivity was found to be high for tests patterns of all orientations except those parallel to the axis of symmetry. This implies that corresponding mirror-orientations (e.g. −45 and +45°) are combined prior to symmetry detection. In Experiment 2, observers detected symmetry in tests of variable orientation in the presence of either non-symmetric or symmetric masks filtered for orientations either parallel or perpendicular to the axis. Observers were found to be primarily affected by masks of the same orientation as the test, thus suggesting that symmetry is computed separately in distinct mirror-orientation channels. In Experiment 3, observers detected a symmetric test of variable height and width embedded in random noise. Data revealed that mirror symmetry is computed over a spatial integration region (IR) that remains approximately constant in area but whose height-to-width aspect ratio changes from 20:1 to 2:1 as orientation is varied from parallel to perpendicular to the axis. We compare human data against that of an ideal observer to identify key factors that limit visual performance and discuss the implications for the functional architecture of symmetry perception. We also propose a multi-channel model of symmetry detection that combines the output of oriented spatial filters in a simple and physiologically plausible manner. Particular emphasis is placed on the notion that changes in the shape of the IR with orientation compensate for changes in information density and partially equate performance across orientations. © 2000 Elsevier Science Ltd. All rights reserved.
PII: S0925-4773(02)00185-5

The vertebrate Six3 gene a homeobox gene of the Six-family, plays a crucial role in early eye and forebrain development. Here we report the isolation of candidate factors that interact with Six3 in a yeast two-hybrid screen. Among these are two basic helix loop helix (bHLH) domain containing proteins. Biochemical analysis reveals that the bHLH proteins ATH5, ATH3, NEUROD as well as ASH1 interact specifically with XSix3. By defining the interacting domains we show that the bHLH domain of NEUROD interacts with the SIX domain of XSix3. The co-expression of the interacting molecules during late retina determination/differentiation suggests a new role for Six3 and the respective interaction partner also in these late steps of eye development. q 2002 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(99)00315-9

The Drosophila tracheal system arises from clusters of ectodermal cells that invaginate and migrate to originate a network of epithelial tubes. Genetic analyses have identi®ed several genes that are speci®cally expressed in the tracheal cells and are required for tracheal development. Among them, trachealess (trh) is able to induce ectopic tracheal pits and therefore it has been suggested that it would act as an inducer of tracheal cell fates; however, this capacity appears to be spatially restricted. Here we analyze the expression of the tracheal speci®c genes in the early steps of tracheal development and their cross-interactions. We ®nd that there is a set of primary genes including trh and ventral veinless (vvl) whose expression does not depend on any other tracheal gene and a set of downstream genes whose expression requires different combinations of the primary genes. We also ®nd that the combined expression of primary genes is suf®cient to induce some downstream genes but not others. These results indicate that there is not a single master gene responsible for the appropriate expression of the tracheal genes and support a model where tracheal cell fates are induced by the co-operation of several factors rather than by the activity of a single tracheal inducer. q 2000 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(00)00586-4

We have recently reported the preliminary characterisation of a novel EGF-related gene, Scube1 (signal peptide-CUB domain-EGFrelated, gene 1), that is expressed prominently in the developing gonad, nervous system, somites, surface ectoderm and limb buds of the mouse. Here we describe the expression pattern of a closely related gene, Scube2 (also known as Cegp1), which maps to the distal region of mouse chromosome 7. Scube2 transcription is restricted to the embryonic neurectoderm but is also detectable in the adult heart, lung and testis. q 2001 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(01)00296-9

In this study we describe cloning and expression of CSAL2, a second member of the spalt gene family in chick. All spalt proteins are characterized by the presence of multiple zinc-®nger motifs, which are highly conserved. Mutations in HSAL1, a human spalt gene result in Townes±Brocks syndrome (TBS). We show here that CSAL2 is expressed in many of the tissues affected in TBS, including neural tissue, limb buds, mesonephros and cloaca. q 2001 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(02)00115-6

ADAMTS1/METH1 belongs to the ADAMTS (a disintegrin and metalloprotease with thrombospondin repeats) family of proteins that currently comprises 18 members. Targeted inactivation of the ADAMTS1 gene results in morphological defects in the kidney, adrenal gland, and adipose tissue in addition to growth retardation and infertility in females. To gain further insight on the biology of ADAMTS1, we examined its expression pattern in the developing mouse from embryonic day 10 (E10) to E18. Expression analysis by RNase protection assays revealed detectable levels of ADAMTS1 transcripts in E10–E18 yolk sac, placenta, brain, heart, lung, limb bud, liver, spleen, and kidney, with much lower levels in the adult. Using in situ hybridization, we have localized ADAMTS1 transcripts predominantly to the epithelium of the developing lung, pancreas, kidney and to a subset of neurons in a temporally restricted manner. Expression was also detected in the tunica media of the aorta, pulmonary, and hepatic vessels. q 2002 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(00)00479-2

Here we describe and compare the expression patterns of the murine genes Lhx2 and Msx1 and their Drosophila orthologues apterous (ap) and muscle-segment homeobox (msh). We ®nd that Lhx2 and Msx1 show complementary patterns of expression in most tissues including the neural and cranial epithelium, pituitary gland, olfactory organs, and neural tube; in contrast, Lhx2 and Msx1 are coexpressed in the developing limbs. Strikingly, the spatial relationship between ap and msh expression in Drosophila is very reminiscent of the expression of their murine orthologues. ap and msh show complementary expression in the leg and antennal imaginal discs, brain and ventral ganglion of the central nervous system (CNS), but both are coexpressed in the wing imaginal disc. These observations suggest conservation in the regulation of these genes between Drosophila and mice. q 2000 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(00)00412-3

The Snail family of genes comprise a group of transcription factors with characteristic zinc ®nger motifs. One of the members of this family is the Slug gene. Slug has been implicated in the development of neural crest in chick and Xenopus by antisense loss of function experiments. Here, we have generated functional derivatives of Xslug by constructing cDNAs that encode the Xslug protein fused with the transactivation domain of the virus-derived VP16 activator or with the repressor domain of the Drosophila Engrailed protein. Our results suggest that Xslug normally functions as a transcriptional repressor and that Xslug-VP16 behaves as a dominant negative of Xslug. In the present work, we con®rm and extend previous results that suggest that Xslug has an important function in neural crest development, by controlling its own transcription. In addition we have uncovered a new function for Xslug. We show that Xslug is expressed in the dorsal mesendoderm at the beginning of gastrulation, where is it able to upregulate the expression of dorsal genes. On the other hand when Xslug is expressed outside of the organizer it represses the expression of ventral genes. Our results indicate that this effect on mesodermal patterning depends on BMP activity, showing that Xslug can directly control the transcription of BMP-4. q 2000 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(99)00296-8

During the initial stages of vertebrate retinogenesis, cells of the optic vesicle adopt one of two alternate cell fates. Cells in the distal-most part of the vesicle, immediately beneath the surface ectoderm, undergo neural differentiation; cells in the proximal part differentiate into retinal pigmented epithelial cells. The mechanisms that establish this pattern of differentiation are poorly understood. In the mouse embryo, Msx2, a homeobox-containing transcription factor, is expressed in cells of the optic vesicle that will form the neural retina, whilst the developing retinal pigmented epithelium (RPE) does not express this gene. Msx2 could therefore be involved in patterning the optic vesicle into neural and pigmented domains. To explore this possibility we ectopically expressed mouse Msx2 in cultures of chick RPE cells. Compared with cultures transfected with a control construct, Msx2-transfected cultures contained fewer cells expressing the RPE marker, Mitf, and more cells expressing class III b-tubulin, a neuronal marker. In addition a small proportion of Msx2-transfected cells acquired a neural-like morphology. These results show that Msx2 can suppress the differentiated state of RPE cells and promote their differentiation into neural cell types. We suggest that Msx2 may pattern the optic vesicle into neural and pigmented domains by affecting the balance between RPE and neural retina differentiation. q 2000 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0042-6989(98)00105-9

We investigate the interaction of atrial natriuretic peptide (ANP), brain natriuretic peptide (BNP) and C-type natriuretic peptide (CNP) with their receptors (NPRA, NPRB and NPRC), as well as the proportion and localization of those receptors in the rat ciliary body. Binding assays and affinity cross-linking experiments demonstrated the presence of the NPRC receptor type. However, the three natriuretic peptides stimulate the guanylate cyclase activity in the ciliary body membranes suggesting the presence of the NPRA and NPRB receptor type. Microautoradiographic data show that the NPRs are localized in the whole ciliary body. Our results indicated that NPRC is the most prominent receptor type in this tissue. © 1998 Elsevier Science Ltd. All rights reserved.
PII: S0925-4773(99)00041-6

The gene Toll (Tl) encodes a maternally supplied interleukin 1 receptor-related transmembrane protein, a key component required to establish dorsoventral polarity in the Drosophila embryo. We have isolated Tl homologs of a primitive dipteran, Clogmia albipunctata, and of the beetle Tribolium castaneum. Tribolium Tl protein (Tl) lacks sequences in the C-terminal portion of the cytoplasmic domains that are conserved in the dipteran homologs. Tl lacking these sequences mediates the ventralizing activity when expressed as a gain-of-function variant in transgenic Drosophila, indicating that the sequences conserved in the Diptera are not essential for Tl signaling. In contrast to Drosophila where Tl gene expression occurs maternally and supplies uniformly distributed Tl in the egg membrane, Tl transcripts form a ventral-to-dorsal gradient in the Tribolium blastoderm stage embryo. This localized expression pattern of Tl transcripts, as compared with the strong maternal and ubiquitous expression in Drosophila and Clogmia embryos, suggests that dorsoventral patterning in long-germ band and short-germ band insects involves the same components but different modes of their action. q 1999 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(02)00086-2

Proteins related to the human transcription factor Sp1 are characterized by the presence of a highly conserved zinc finger domain consisting of three C2H2 type zinc fingers. Here we describe two Xenopus laevis cDNAs, which encode novel Sp1-related C2H2 type zinc finger transcription factors named XSPR-1 and XSPR-2. Structurally, XSPR-1 and XSPR-2 are closely related to the murine Sp5, which interacts genetically with Brachyury (Dev. Biol. 227 (2000) 358). XSPR-1 and XSPR-2 are expressed in broad and dynamic patterns during early development. Starting at gastrulation, XSPR-1 transcripts are restricted to the non-involuting marginal zone, and, at later stages, to the neuroectoderm, forebrain, otic vesicles and the midbrain/hindbrain boundary. In contrast, XSPR-2 expression is found predominantly within the presumptive mesoderm during gastrulation. At tailbud and tadpole stages, XSPR-2 is expressed exclusively in the tip of the tail. q 2002 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(99)00144-6

Hypoxia inducible factors (HIF) are candidate transcriptional regulators of vascular development. Unlike HIF-1a ± the founding member of the HIF family ± which is expressed more or less ubiquitously, HIF-2a (also called HRF, HLF and EPAS1) is highly expressed by vascular endothelial cells and was shown to activate the transcription of endothelial cell-speci®c receptor tyrosine kinases (tie-2 and ̄k-1/VEGF receptor 2) and of vascular endothelial growth factor (VEGF). Therefore HIF-2a is a candidate dual regulator of vascular development. Here we describe the quail homologue of HIF-2a . Sequence analysis reveals that HIF-2a is highly conserved between birds and mammals. Like the murine HIF-2a , the quail molecule is highly expressed by endothelial cells but also detectable in certain epithelial cells such as in the endoderm. q 1999 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(01)00389-6

Endogenous histamine is involved in tissue growth and cell proliferation. In accordance with a putative function of the H3 receptor in this mitogenic effect, we show that H3-receptor mRNAs are expressed together with those of the histamine-synthesizing enzyme in the embryonic liver and adipose tissue, and in various epithelia. Finally, we show that activation of recombinant H3 receptors enhances MAP kinase activity. q 2001 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0925-4773(02)00040-0

Members of the T-box (tbx) gene family encode developmentally regulated transcription factors, several of which are implicated in human hereditary diseases. We have cloned the paralogous genes tbx15 and tbx18 in zebrafish and have characterised their expression in detail. tbx15 is expressed in paraxial head mesenchyme and its derivatives, the extraocular and jaw musculature and the posterior neurocranium. Further areas of tbx15 expression are in the anterior somitic mesoderm, in periocular mesenchyme and in the pectoral fin mesenchyme throughout larval development. Areas of strong tbx18 expression are found in the developing somitic and presomitic mesoderm, in the heart and in pectoral fin mesenchyme, as well as the ventral neuroectoderm and the developing palate. Both genes exhibit particular differences in expression compared to their murine orthologs. q 2002 Elsevier Science Ireland Ltd. All rights reserved.
PII: S0042-6989(98)00118-7

Disparity discrimination thresholds are known to increase with both retinal eccentricity and distance from the horopter. However, little is known about how the detectability of cyclopean gratings varies with retinal position. Thresholds for disparity corrugations were measured as a function of corrugation frequency for different visual eccentricities. Subjects viewed annular displays of random dot stereograms, and judged in which of two intervals a circumferential disparity modulation was present. For any given eccentricity, visual sensitivity to disparity corrugations was bandpass. As eccentricity increased from 3.5 to 21.0°, peak-to-trough thresholds were found to increase, the optimal corrugation frequency for detection decreased, and the upper cutoff corrugation frequency also decreased. The M-Scaling functions of Rovamo and Virsu were used to replot the data in terms of cycles per unit cortical distance. Peak detection frequency was constant at 0.8 cycles per mm of cortex after this rescaling, demonstrating that acuity for disparity modulations is approximately M-scaled beyond the fovea. © 1998 Published by Elsevier Science Ltd. All rights reserved.
PII: S0925-4773(01)00312-4

castor (cas) encodes a zink ®nger protein expressed in a subset of Drosophila embryonic neuroglioblasts where it controls neuronal differentiation. We show here that cas is expressed at larval and pupal stages in brain cell clusters where it participates in the elaboration of the adult structures. In particular using the MARCM system (mosaic analysis with a repressible cell marker), we show that cas is required postembryonically for correct axon path®nding of the central complex (CX) and mushroom body (MB) neurons. The linotte (lio) gene encodes a transmembrane protein expressed at larval/pupal stage in a glial structure, the TIFR, and interacts with the no-bridge (nob) gene. We show that cas interacts genetically with lio and nob. These interactions do not involve direct transcription regulation but probably cellular communication processes. q 2001 Elsevier Science Ireland Ltd. All rights reserved.