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1 ecific peptide/MHC ligation of the alphabeta clonotype.
2 at were comparable to those of the effective clonotype.
3 explaining the immunodominant usage of this clonotype.
4 age-dependent increase in a diabetogenic CD8 clonotype.
5 e observed long-term persistence of a single clonotype.
6 tributing to the selection of the public TCR clonotype.
7 tted uninhibited accumulation of low-avidity clonotypes.
8 3s that group into 30 distinct antibody V(H) clonotypes.
9 by length-matched Ag-specific CD8(+) T-cell clonotypes.
10 d proliferation (LIP) of two distinct T cell clonotypes.
11 ease disproportionally affects low-frequency clonotypes.
12 for cross-recognition compared with dominant clonotypes.
13 nes per response, of both public and private clonotypes.
14 ocess, conditioned on non-extinction of both clonotypes.
15 the numbers of T cells belonging to the two clonotypes.
16 structural role for the TCRA chain for these clonotypes.
17 t of the repertoire implies a role for these clonotypes.
18 d CD4 T cell response toward higher-affinity clonotypes.
19 itical for recognition by most of the T cell clonotypes.
20 inant as well as a nonexpanded, "supporting" clonotypes.
21 neity exists within individual CD8(+) T cell clonotypes.
22 ong behavior of CMV- and EBV-specific T cell clonotypes.
23 ents identified no additional cross-reactive clonotypes.
24 CDR3 motifs, and a high frequency of public clonotypes.
25 rare, found in only one of seven VH1-46 IgG clonotypes.
26 ogenic neoantigens and tumor-reactive T cell clonotypes.
27 r repertoires comprising exclusively private clonotypes.
28 he major part of the differences among these clonotypes.
31 influenza vaccine, with boosted pre-existing clonotypes accounting for approximately 60% of the respo
33 To evaluate the dynamic nature of T cell clonotypes across time, we utilized several binary simil
34 ssential for the maintenance of low-affinity clonotypes after protein vaccination but was not suffici
39 ll patients within 10 d of infusion, and TCR clonotype analysis showed persistence of infused cells i
40 were dispensable for the development of this clonotype and had negligible impact on the polyclonal Tr
42 ies; a decrease in or loss of the pathogenic clonotype and restoration of the TCR repertoire was foun
43 ntained over time by a recruitment of non-RS-clonotypes and a shift of existing RS-clonotypes into hi
44 d similarity between multiple immunodominant clonotypes and codominant as well as a nonexpanded, "sup
45 y IgM(+) B cells were related to some IgA(+) clonotypes and switched to IgA in response to T cell-ind
47 NA sequencing procedures for identifying TCR clonotypes and transcript phenotypes in individual T cel
48 arthritis model to determine the frequency, clonotype, and specificity of T cells that infiltrate ar
49 d not cause the elimination of high-affinity clonotypes, and at a low dose, they also skewed CD4 T ce
50 rior Ag exposure, inferred from expanded TCR clonotypes, and essential phenotypic properties in their
51 er C127 expression compared with subdominant clonotypes, and TCR avidity positively correlates with P
52 sms: 1) functional improvement of persisting clonotypes; and 2) recruitment of particular clonotypes
53 t the persistence of numerous BM plasma cell clonotypes ( approximately 2%) identifiable at all point
56 nd sequencing indicated that distinct T-cell clonotypes are preferentially increased in the CNS compa
57 may maintain TCR diversity and that dominant clonotypes are sensitive to antigen even after dramatic
59 te that the specificity of individual T cell clonotypes arises not only from TCR residues that create
60 ns for the number of cells belonging to each clonotype as well as a linear Fokker-Planck equation for
61 e emergence of high-avidity Melan-A-specific clonotypes as a surrogate marker of treatment efficacy.
62 )-primed mice that appears to be the "public clonotype" as it expanded in response to peptide in all
66 en by preferential expansion of high avidity clonotypes at the expense of their low avidity counterpa
68 R3, and a remarkable sharing of one dominant clonotype between individual old mice, implying operatio
69 lates, reveal that effective and ineffective clonotypes bind to the terminal portions of the peptide-
70 al susceptibility varied substantially among clonotypes but was consistent across different locations
71 nsistent with the hypothesis that the public clonotype BV8S2/BJ2S7 is a driver of disease and necessa
72 elevated levels of expression of BCR in this clonotype by making the transgenic Igh locus homozygous.
75 ity of the AI4 TCR, as the selection of this clonotype can be influenced by multiple MHC molecules, i
78 E. coli, subspecies-level identification by clonotyping can be used to significantly improve empiric
79 action (<5%) of peripheral blood plasmablast clonotypes (CD3(-)CD14(-)CD19(+)CD27(++)CD38(++)CD20(-)T
81 oires, we observed that germline-encoded TCR clonotypes, characteristic of neonatal infection, persis
82 with distinct T cell antigen receptor (TCR) clonotypes, characterized by superior control of HIV-1 r
83 using graph theory, with the cross-reactive clonotypes connecting the different HLA-A2 peptides reco
86 ction, explaining how Gag293-specific public clonotypes could be selected in individuals with diverse
87 tricate than previously described, and all 3 clonotypes (CPC, FL, t-FL) may occur simultaneously with
91 minate between pathogen-derived ligands in a clonotype-dependent manner, providing a basis for adapti
96 dy, we performed in-depth analysis of T cell clonotypes directed against a dominantly recognized HLA
98 roliferation phase during which low-affinity clonotypes disappeared despite exhibiting no sign of enh
99 quency analysis shows the same two-component clonotype distribution described earlier for these reper
101 lthough the repertoires show broadly similar clonotype distributions, the number of observable clonot
103 elies on the recruitment of antigen-specific clonotypes, each defined by the expression of a distinct
104 o/8/1934 and Staphylococcus aureus USA300, a clonotype emerging as a leading contributor in postinflu
105 ant targeted reductions in the expression of clonotypes encoded by 14 specific Vkappa genes with the
106 clonotypes; and 2) recruitment of particular clonotypes endowed with superior functional capabilities
107 med in a prospective vaccine trial, in which clonotype engagement was governed by the nature of the a
108 s modulated by diverse T cell receptor (TCR) clonotypes engaging peptide-MHC class I complexes on inf
109 were significantly correlated with specific clonotypes, especially with CH40-30 (also known as H30),
115 revealed that a dominant public CD4(+) Treg clonotype expressing Vbeta14-Jbeta1.2 with a CDR3 length
117 sed CD4 T cell response toward high-affinity clonotypes expressing restricted public TCR, whereas pep
119 In the mean field approximation we show that clonotype extinction is certain and compute mean extinct
121 The first component includes lower frequency clonotypes for which distribution can be described by a
123 irs were Valpha3.2(3.5)/Vbeta14, a prominent clonotype found in the poly(F,Y,A,K)n-specific T cell li
124 P = 0.02), decreases in the number of T-cell clonotypes found within epitope-specific T cell receptor
125 in the liver than in the blood, and the peak clonotype frequency was concurrent with the peak viral l
127 ects the transfer of epitope-specific T-cell clonotypes from donor to recipient; (3) less differentia
128 ctivity and identified gluten-induced T-cell clonotypes from total blood and gut TCR repertoires in a
129 d subsequent activation of the CD8(+) T-cell clonotype G9C8, which recognizes insulin B15-23 via an a
132 ssed by the dominant dextran-specific B-cell clonotype had no effect upon the magnitude of the normal
133 eptide demonstrated that Tp2(49-59)-specific clonotypes had a broad range of fine specificities for t
139 onses, we compared the T cell receptor (TCR) clonotype in parent and hybrid strains of respiratory sy
143 strate liver-infiltrating disease-associated clonotypes in all three diseases evaluated, and evidence
144 methods for the detection of immunodominant clonotypes in blood and in historic marrow biopsies of 3
145 ed oligoclonal expansion of specific TCRbeta clonotypes in CD8(+)PD-1(+) compared with CD8(+)PD-1- TI
147 the role of individual T-cell receptor (TCR) clonotypes in differential antiviral CD8(+) T-cell funct
148 dance analysis, we identified gluten-induced clonotypes in each patient that were composed of a large
149 monitor the levels of putative allospecific clonotypes in posttransplant blood samples and subsequen
150 the development and maintenance of neonatal clonotypes in the brain and spleen of mice during chroni
151 urthermore, the most highly expanded TCRbeta clonotypes in the CD8(+) and the CD8(+)PD-1(+) populatio
155 LA-A2 adult subjects, we identified the BV19 clonotypes in the recall response to the influenza epito
156 bit negligible competition with other T cell clonotypes in the repertoire, since this case provides a
157 ssue was used to quantitate and track T-cell clonotypes in these treated subjects with prostate cance
159 ortion of the homologous CD8(+) EBV-specific clonotypes, in the "fluctuant" group was substantial hig
160 imumab triggered increases in the numbers of clonotypes, including newly detected clones and a declin
161 anisms that blocked the local propagation of clonotypes independently of antigen dose and not as a co
162 und that the predominant conventional T cell clonotypes infiltrating target lesions express antigen r
163 ation of MHC promiscuous autoreactive CD4(+) clonotypes into antidiabetogenic autoregulatory T cells.
167 We prove that the ultimate fate of both clonotypes is extinction and provide a bound on mean ext
171 ne the antibody repertoire at the individual clonotype level in the sera of young adults before and a
174 ) T-LGL leukemia and suggest that many T-LGL clonotypes may be private to the disease and may not be
176 and suggest that cross-reactive, subdominant clonotypes may retain greater capacity to suppress repli
177 be cross-recognized by identical CD8 T cell clonotypes mobilized in vivo, yet even subtle difference
178 ments to sequencing reads and assembling the clonotypes, most of them are not designed to track and e
179 of innate B-1 cells and secretion of T15/EO6 clonotype natural IgM antibodies, which bind the PC of O
180 including singletons, i.e., the fraction of clonotypes observed only once, and repertoire diversity.
182 ment of T-cell receptor (TCR) alpha and beta clonotypes of the initial HIV-1-specific CD8(+) T cells
185 cines may expand distinct Ag-specific T cell clonotypes or induce disparate degrees of protection are
186 tween HIV-1 and virus-specific CD8(+) T-cell clonotypes orchestrated at the TCR-antigen interface.
189 the thymus, before any exposure to antigen, clonotype-positive T reg and T conv cells express a seco
190 Escherichia coli species into clonal groups (clonotypes) predicts antimicrobial susceptibility or cli
192 s representing variant epitopes, subdominant clonotypes produce higher relative levels of cytokines a
193 ation of MHC-promiscuous autoreactive T-cell clonotypes, promoting their deviation into autoregulator
194 ble family genes encoded the same amino acid clonotypes, providing additional support for antigen-dri
195 rms of the self-antigens they recognise, one clonotype quickly becomes extinct in a process resemblin
196 se TCR repertoire comprising several private clonotypes rarely observed in control mice or in the pre
200 verall hierarchy of dominant T cell receptor clonotypes remained stable compared to that pre-ART.
201 c virus type 1; (ii) T cell antigen receptor clonotype repertoires; and (iii) microbial data from inf
203 an be complex, composed of a large number of clonotypes represented at low copy numbers, while mainta
204 equences were extremely diverse, without any clonotype representing more than 2% of the overall TCR p
205 ing within an individual reveals private AST clonotypes resident in the memory population, as would b
207 minant alloreactive clones; 10 corresponding clonotypes restricted to activated T cells were identifi
209 ective alleles' is modulated by specific TCR clonotypes selected during natural infection, which prov
210 e NY-ESO-1-specific and TRAG-3-specific Treg clonotypes share a common TCR CDR3 Vbeta usage with Foxp
214 tained the initial advantage of high-avidity clonotypes, slower completion permitted uninhibited accu
215 gate TCR-pMHC interactions from multiple CTL clonotypes specific for a well-defined HIV-1 epitope.
219 igen-specific T regs maintain high levels of clonotype-specific T cell receptor expression and exert
220 f the individual, as evidenced by discordant clonotype-specific transitions directed against differen
223 proportion of polyreactive and self-reactive clonotypes, suggesting that activation checkpoints exist
225 ance hinder the contribution of high-avidity clonotypes targeting residues 206-214 of islet-specific
228 cribed an Ig-transgenic, autoreactive B cell clonotype that undergoes a novel tolerance pathway.
229 competition process between a pair of T cell clonotypes that are similar in terms of the self-antigen
230 ymic development producing individual T cell clonotypes that express TCRs with unique patterns of Ag
231 es that were longer than telomeres of T cell clonotypes that failed to persist (6.2 vs 4.5 kb, respec
232 e skewing and the presence of high-frequency clonotypes that had undergone significant in vivo expans
233 hierarchy of recurrence rates for individual clonotypes that is determined by relative production fre
234 ure of the memory repertoire and whether the clonotypes that make up the repertoire decay at random.
235 Furthermore, individual TIL-derived T cell clonotypes that persisted in vivo following adoptive cel
237 accination by electroporation primed for TCR clonotypes that were associated with HIV control, highli
240 erum repertoire comprised between 40 and 147 clonotypes that were specific to each of the three monov
241 xposure identified subsets of highly similar clonotypes, the most proliferative of which showing sign
242 olerance, we followed the behavior of BDC2.5 clonotype thymocytes in fetal thymic organ cultures (FTO
243 , hence, avidity for autoantigen allows this clonotype to bypass conventional tolerance mechanisms.
244 phenotype, trafficking of the same expanded clonotype to different regions of the kidney and to the
245 acy is inherently dynamic, allowing each TCR clonotype to have a wide range of agonists while avoidin
247 ion profiles of dominant and subdominant TCR clonotypes to evaluate the relationship between the comp
249 Interestingly, antigen-specific Th cell clonotypes unevenly assort into these peripheral compart
250 e profound expansion and shrinkage of T cell clonotypes upon antigenic triggering and, more important
251 ther than the context of exposure and public clonotype usage was associated with enhanced recognition
253 is of responses to B51-TI8 revealed a public clonotype using TRAV17/TRBV7-3 TCR genes in six out of s
255 us sequence variant, another circulating TCR clonotype was able to preferentially recognize the varia
258 nother viral challenge, the rebound of these clonotypes was seen prior to an appreciable reconstituti
259 Based on the sequence of immunodominant CDR3 clonotypes, we designed quantitative assays for monitori
260 the methods used to identify immunodominant clonotypes, we were able to follow the behavior of poten
261 es characteristic of the highly autoreactive clonotype were not reversed by an intrinsic FcgammaRIIB
262 r TV9 and the characteristics of constituent clonotypes were assessed by ex vivo priming of circulati
265 In contrast, BV16/BJ2S5 and numerous private clonotypes were either Th1 or Th2 and persisted followin
266 en primary Ab-forming cell responses of both clonotypes were equivalently increased by such a deficie
269 We found that cross-reactive CD8+ T cell clonotypes were mobilized to counter the rapid emergence
270 esolved infection, identical T cell receptor clonotypes were present in liver and peripheral blood.
272 o thymic involution, a substantial number of clonotypes were stable, e.g., detected at two times.
273 cy and the number of Gag CM9-specific public clonotypes were strongly correlated with VIA mediated by
276 son, antibodies with 18 different CDRH3s (12 clonotypes) were represented in the antigen-specific IgG
277 mory CD4 TCR repertoire toward high-affinity clonotypes whereas protein vaccines maintained low-affin
278 ifferential testing enabled the detection of clonotypes which were significantly changed across time.
279 e early mobilization of public CD8(+) T-cell clonotypes, which can exert profound biological effects
280 unity at the level of individual constituent clonotypes, which were identified according to the expre
281 etramers to selectively eradicate pathogenic clonotypes while leaving overall T-cell immunity intact.
282 ertoire structure might provide a panoply of clonotypes whose differential avidity for the epitope wo
283 0 of the most representative public TCR beta clonotypes, whose abundance among the top 100,000 clones
287 less, certain public and conserved CDR3alpha clonotypes with distinct molecular signatures were ident
288 ntigens for the selection of superior T-cell clonotypes with enhanced antigen recognition properties.
291 Together, these findings indicate that TCR clonotypes with superior functions are associated with H
292 CH typing divided the isolates into >200 CH clonotypes, with 93% of the isolates belonging to clonot
293 ertoire comprises approximately 100 antibody clonotypes, with three clonotypes accounting for >40% of
295 1 was expressed at higher levels on dominant clonotypes within epitope-specific responses before and
296 ion of PD-1 on T cell populations and T cell clonotypes within epitope-specific responses from these
298 o decryption by interrogation of constituent clonotypes within the antigen-experienced T cell pools.
299 agnitude, the efficacy of constituent T-cell clonotypes within the primed population can be poor.
300 ) T cells, we hypothesized that neonatal TCR clonotypes would be locked in the brain and persist into
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