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Subterranean phylogeography of freshwater crayfishes shows extensive gene flow and surprisingly large population sizes.

Subterranean animals are currently viewed as highly imperiled, precariously avoiding extinction in an extreme environment of darkness. This assumption is based on a hypothesis that the reduction in visual systems and morphology common in cave faunas reflects a genetic inability to adapt and persist coupled with the perception of a habitat that is limited, disconnected, and fragile. Accordingly, 95% of cave fauna in the United States are presumed endangered due to surface environmental degradation and limited geographic distributions. Our study explores the subterranean phylogeography of stygobitic crayfishes in the southeastern United States, a global hotspot of groundwater biodiversity, using extensive geographic sampling and molecular data. Despite their endangered status, our results show that subterranean crayfish species have attained moderate to high levels of genetic diversity over their evolutionary histories with large population sizes and extensive gene flow among karst systems. We then compare the subterranean population histories to those of common surface stream-dwelling crayfishes. Our results show recent drastic declines in genetic variability in the surface crayfish and suggest that these species also warrant conservation attention.

Animals↗

Amplification and loss of dihydrofolate reductase genes in a Chinese hamster ovary cell line.

During stepwise increases in the methotrexate concentration in culture medium, we selected Chinese hamster ovary cells that contained elevated dihydrofolate reductase levels which were proportional to the number of dihydrofolate reductase gene copies (i.e., gene amplification). We studied the dihydrofolate reductase levels in individual cells that underwent the initial steps of methotrexate resistance by using the fluorescence-activated cell sorter technique. Such cells constituted a heterogeneous population with differing dihydrofolate reductase levels, and they characteristically lost the elevated enzyme levels when they were grown in the absence of methotrexate. The progeny of individual cells with high enzyme levels behaved differently and could lose all or variable numbers of the amplified genes.

Animals↗

Effect of 5-fluorouracil on carcinoembryonic antigen expression and shedding at clonal level in colon cancer cells.

BACKGROUND: The carcinoembryonic antigen (CEA) is a tumor marker largely utilized for the detection of minimal disease or as a target of immunotherapeutic approaches. In preclinical models CEA has been found to be up-regulated after exposure of cancer cells to 5-fluorouracil (5-FU). In the present study, the clonal distribution of CEA and its regulation by 5-FU at clonal level was investigated using human HT-29 colon cancer cells. MATERIALS AND METHODS: The extent of CEA expression was measured in terms of: (a) antigen levels on plasma membrane, by flow cytometry; (b) cytoplasm and membrane protein, by Western blot analysis: (c) transcript, by Northern blot analysis; (d) CEA shedding by radioimmunossay. RESULTS: CEA protein and gene transcript were variably expressed among different clones. In all cases 5-FU was able to increase the percentage of CEA-positive cells, the amount of antigen, either in the membrane or cytosolic fractions, and the corresponding transcript. Moreover, a marked increase of CEA shedding was found in drug-treated cells with respect to that of controls. The increase of CEA induced by the antimetabolite was not the result of a selection mechanism based on preferential killing of CEA negative cells. The antimetabolite was capable of enhancing antigen expression also in other CEA-positive tumor cell lines with different basal levels of the marker. CONCLUSIONS: The present findings could be of potential value to increase the sensitivity of diagnostic procedures based on detection of CEA positive tumor cells. Moreover, the antimetabolite might be included in immunotherapeutic protocols to facilitate recognition of CEA-positive cancer cells by immune responses.

Antimetabolites, Antineoplastic↗

cDNA cloning and sequencing of a novel monoclonal antibody to carcinoembryonic antigen and construction of a mouse/human chimeric antibody.

BACKGROUND: Mouse monoclonal antibody F33-104 recognizes an epitope which is present on the carcinoembryonic antigen (CEA) molecule but not on the other CEA family member proteins, and which seems to be of potential value for immunotherapy of CEA-expressing cancers. However, an inherent problem in its in vivo application is the human anti-mouse antibody response. MATERIALS AND METHODS: To reduce its immunogenicity in humans, we cloned and sequenced the V region genes of heavy and light chains of F33-104 using the reverse transcription-polymerase chain reaction method, and then constructed a mouse/human chimeric antibody, designated Ch F33-104, by fusing the F33-104 VH and V kappa genes to human C gamma 1 and C kappa genes, respectively. The resulting Ch F33-104 was expressed in non-Ig-producing myeloma cells and characterized for its CEA binding specificity and the tumor cell killing activity. RESULTS: Ch F33-104 specifically bound to CEA-expressing tumor cells and revealed a potent antibody-dependent cell-mediated cytotoxicity with human lymphokine-activated killer cells as effectors against the CEA-expressing tumor cells. CONCLUSION: This mouse/human chimeric antibody could therefore be a candidate for cancer immunotherapy of CEA-positive cancers.

Amino Acid Sequence↗

Phylogeography of the planktonic chaetognath Sagitta setosa reveals isolation in European seas.

Numerous planktonic species have disjunct distribution patterns in the world's oceans. However, it is unclear whether these are truly unconnected by gene flow, or whether they are composed of morphologically cryptic species. The marine planktonic chaetognath Sagitta setosa Müller has a discontinuous geographic distribution over the continental shelf in the northeastern Atlantic, Mediterranean Sea, and Black Sea. Morphological variation between these populations has been described, but overlaps and is therefore unsuitable to determine the degree of isolation between populations. To test whether disjunct populations are also genetically disjunct, we sequenced a 504-bp fragment of mitochondrial DNA comprising the cytochrome oxidase II region of 86 individuals. Sequences were highly variable; each represented a different haplotype. Within S. setosa, sequence divergence ranged from 0.2 to 8.1% and strong phylogeographic structure was found, with four main groups corresponding to the northeastern Atlantic, Mediterranean Sea (including Ligurian Sea, Tyrrhenian Sea and Gulf of Gabes), Adriatic Sea, and Black Sea. Two of these (Atlantic and Black Sea) were resolved as monophyletic clades, thus gene flow between disjunct populations of S. setosa has been extremely limited and lineage sorting has taken place. The deepest divergence was between Atlantic and Mediterranean/Black Sea populations followed by a split between Mediterranean and Black Sea populations. The Mediterranean/Black Sea clade comprised three groups, with the Adriatic Sea as the most likely sister clade of the Black Sea. These data are consistent with a colonization of the Black Sea from the Mediterranean. Furthermore, a possible cryptic species was found in the Black Sea with 23.1% sequence divergence from S. setosa. Two possibilities for the evolutionary origin of this species are proposed, namely, that it represents a relict species from the ancient Paratethys, or that it represents another chaetognath species that colonized the Black Sea more recently. Even though the exact timing of disjunction of S. setosa populations remains unclear, on the basis of the geological and paleoclimatic history of the European basins and our estimates of net nucleotide divergence, we suggest that disjunct populations arose through vicariance resulting from the cyclical changes in temperature and sea levels during the Pleistocene. We conclude that these populations have remained disjunct, not because of limited dispersal ability, but because of the inability to maintain viable populations in suboptimal, geographically intermediate areas.

Animals↗

Conservation genetics of the wood ant, Formica lugubris, in a fragmented landscape.

Various intrinsic factors connected to the special features of sociality influence the persistence of social insect populations, including low effective population size, reduced amount of genetic variation easily leading to inbreeding depression, and spatially structured populations. In this work, we studied an isolated, small and fragmented population system of the red wood ant Formica lugubris, and evaluated the impact of social and genetic population structure on the persistence and conservation of the populations. The effective population size was large in our study population because all nests were polygynous. As a result, and despite the apparent isolation, the amount of nuclear genetic variability was similar to that in a nonisolated population system. Lack of inbreeding, as well as a high level of variability, indirectly suggests that this population does not suffer from inbreeding depression. The spatial distribution of genetic variation between local populations suggests intensive, but strongly male-biased, nuclear gene flow. Thus, the persistence of this population system does not seem to be threatened by any immediate social or genetic factor, but colonization of new habitat patches may be difficult because of restricted female dispersal.

Animals↗

Ecological factors influence population genetic structure of European grey wolves.

Although the mechanisms controlling gene flow among populations are particularly important for evolutionary processes, they are still poorly understood, especially in the case of large carnivoran mammals with extensive continuous distributions. We studied the question of factors affecting population genetic structure in the grey wolf, Canis lupus, one of the most mobile terrestrial carnivores. We analysed variability in mitochondrial DNA and 14 microsatellite loci for a sample of 643 individuals from 59 localities representing most of the continuous wolf range in Eastern Europe. We tested an array of geographical, historical and ecological factors to check whether they may explain genetic differentiation among local wolf populations. We showed that wolf populations in Eastern Europe displayed nonrandom spatial genetic structure in the absence of obvious physical barriers to movement. Neither topographic barriers nor past fragmentation could explain spatial genetic structure. However, we found that the genetic differentiation among local populations was correlated with climate, habitat types, and wolf diet composition. This result shows that ecological processes may strongly influence the amount of gene flow among populations. We suggest natal-habitat-biased dispersal as an underlying mechanism linking population ecology with population genetic structure.

Animals↗

Generational variation and stabilization in resynthesized allotetraploid Brassica juncea derived from diploid progenitors B. rapa and B. nigra.

BACKGROUND: Polyploidy is a major driver of plant evolution and crop improvement, generating novel variation in morphology, physiology, and agronomic traits. Brassica juncea (AABB, 2n = 36), a natural allotetraploid derived from B. rapa (AA) and B. nigra (BB), is an important oilseed and vegetable crop; however, its narrow genetic base limits further breeding gains. Resynthesized B. juncea (RBJ), developed from known progenitors, provides a tractable system to investigate polyploid stabilization, trait diversification, and generational variation. This study evaluated RBJ across nine generations (F1-S8) to elucidate generational variation in morphological, molecular, cytological, and oil content traits during progressive stabilization. RESULTS: Substantial variation was observed for key yield-related traits, including siliqua length, seeds per siliqua, and thousand-seed weight. High estimates of heritability, genotypic variance, and genetic advance indicated their potential utility in selection based improvement. Comparative analyses revealed a clear generational progression, characterized by relatively enhanced performance in early generations, increased recombination-driven variability in intermediate generations, and the partial stabilization of several traits in later generations. Generation mean analysis suggested the involvement of additive, dominance, and epistatic gene effects in trait inheritance. Molecular analysis using SSR markers confirmed the amphidiploid origin and genomic integrity of RBJ generations. Cytological assessments, pollen viability assays, and flow cytometric analysis collectively demonstrated stable chromosome numbers, improved fertility, and maintenance of ploidy stability across successive generations. CONCLUSIONS: The study provides valuable insights into the generational variation and stabilization of morphological, molecular, and oil content traits in resynthesized B. juncea. The findings suggest that variability arising from polyploidization and interspecific hybridization undergoes gradual reorganization across successive generations, leading to increased trait stabilization and more consistent expression of selected agronomic characteristics. Collectively, these results contribute to the understanding of early stabilization processes in RBJ, highlighting resynthesized polyploids as useful systems for studying variation and stabilization in allopolyploid crops.

Mustard Plant↗

IgM secretory tailpiece drives multimerisation of bivalent scFv fragments in eukaryotic cells.

BACKGROUND: The monoclonal antibody (mAb) TP-3 binds selectively to human and canine osteosarcoma (OS) cells and is therefore a potential candidate for use as a targeting agent in radioimmunoimaging and therapy of OS metastases. However, intact murine mAbs have several drawbacks such as large size, delayed blood clearance and high immunogenicity, all of which can be overcome by genetic engineering. OBJECTIVES: To construct and express bivalent and multivalent TP-3 scFv fragments from the mammalian expression vector, pLNO. This vector has unique restriction sites for simple cassette cloning of any individual variable (V) and constant (C) genes and has previously been used for expression of intact chimeric TP-3 mAbs and Fab fragments. Furthermore, it is also suitable for expression of any modified V region, such as a scFv fragment, fused to any modified C region or to non-immunoglobulin protein sequences. STUDY DESIGN: Six different constructs were made; three scFv-CH3 fragments that differed in the design of linker between the scFv fragment and the IgG CH3 domain. These constructs were also made with the IgM secretory tailpiece (microtp) attached to the C terminus. RESULTS: All constructs were secreted as bivalent antibody fragments with a molecular weight of about 100 kDa. A band corresponding to a dimer appeared in all the supernatants from TP-3 scFv-CH3 producing cells, whether microtp was present or not, whereas higher orders of multimers were not seen. However, pulse chase analyses of the cells revealed that a small fraction of higher order polymers was formed from genes including the fragment encoding microtp and that microtp conferred retention both to monomers and intermediate polymers. The recombinant TP-3 antibody fragments were shown to bind human OS cells. CONCLUSION: Recombinant mAb fragments can be designed and cloned into the mammalian expression vector, pLNO. This vector is flexible in the sense that the genes encoding such fragments can be expressed from either cDNA or from genomic DNA. A microtp attached to the CH3 domain in these fragments was sufficient to drive polymerization, however inefficiently and intracellular retention of both monomers and intermediate polymers was observed.

Amino Acid Sequence↗

Phenotype and TCR gamma delta variable gene repertoire of intestinal intraepithelial lymphocytes in wild mice (Mus musculus domesticus): abundance of V gamma 1 transcripts and extensive delta gene diversity.

In order to study murine intestinal intraepithelial lymphocytes (IEL) independent of factors imparted by conditions of laboratory housing and breeding, and to provide a basis for comparison of IEL studies between inbred and outbred mouse populations, IEL from the domestic house mouse, Mus musculus domesticus, were analyzed by flow cytometric analyses using mAbs to murine lymphocyte markers, and by polymerase chain reaction to study the TCR gamma and delta V gene repertoires. The majority of IEL in wild mice were CD3+, CD8+CD4- T cells. CD4+CD8- also were present in IEL isolates from wild mice, although at low numbers. Among IEL, but not T cells from the spleen or lymph nodes, there was a notable lack of Thy-1 expression, a preponderance of CD8 alpha alpha + T cells, and a relatively high ratio (3:1) of TCR gamma delta + T cells over TCR alpha beta + T cells, suggesting that some IEL in wild mice may develop via an extrathymic pathway similar to that described for laboratory mice. Analyses of the IEL gamma and delta variable genes revealed rearrangements of three of six V region gamma genes (V gamma 1, V gamma 2, and V gamma 5), with an abundance of V gamma 1 transcripts as determined by Northern blot analyses. For the delta gene, rearrangement of five of seven V region elements had occurred (V delta 2, V delta 3, V delta 4, V delta 5, and V delta 6).(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

Patterns and levels of gene flow in Rhododendron metternichii var. hondoense revealed by microsatellite analysis.

Parentage analysis was conducted to elucidate the patterns and levels of gene flow in Rhododendron metternichii Sieb. et Zucc. var. hondoense Nakai in a 150 x 70 m quadrant in Hiroshima Prefecture, western Japan. The population of R. metternichii occurred as three subpopulations at the study site. Seventy seedlings were randomly collected from each of three 10 x 10 m plots (S1, S2, and S3) on the forest floor of each subpopulation (A1, A2, and A3). Almost all parents (93.8%) of the 70 seedlings were unambiguously identified by using 12 pairs of microsatellite markers. Within the quadrant, adult trees less than 5 m from the centre of the seedling bank (plots S1, S2, and S3) produced large numbers of seedlings. The effects of tree height and distance from the seedling bank on the relative fertilities of adult trees were highly variable among subpopulations because of the differences in population structure near the seedling bank: neither distance nor tree height had any significant effect in subpopulation A1; distance from the seedling bank had a significant effect in subpopulation A2; and tree height had a significant effect in subpopulation A3. Although gene flow within each subpopulation was highly restricted to less than 25 m and gene flow among the three subpopulations was extremely small (0-2%), long-distance gene flow from outside the quadrant reached 50%. This long-distance gene flow may be caused by a combination of topographical and vegetational heterogeneity, differences in flowering phenology, and genetic substructuring within subpopulations.

DNA, Plant↗

Bromodeoxyuridine labeling and flow cytometric identification of replicating Saccharomyces cerevisiae cells: lengths of cell cycle phases and population variability at specific cell cycle positions.

An immunofluorescent staining procedure has been developed to identify, with flow cytometry, replicating cells of Saccharomyces cerevisiae after incorporation of bromodeoxyuridine (BrdUrd) into the DNA. Incorporation of BrdUrd is made possible by using yeast strains with a cloned thymidine kinase gene from the herpes simplex virus. An exposure time of 4 min to BrdUrd results in detectable labeling of the DNA. The BrdUrd/DNA double staining procedure has been optimized and the flow cytometry measurements yield histograms comparable to data typically obtained for mammalian cells. On the basis of the accurate assessment of cell fractions in individual cell cycle phases of the asynchronously growing cell population, the average duration of the cell cycle phases has been evaluated. For a population doubling time of 100 min it was found that cells spend in average 41 min in the replicating phase and 24 min in the G2+M cell cycle period. Assuming that mother cells immediately reenter the S phase after cell division, daughter cells spend 65 min in the G1 cell cycle phase. Together with the single cell fluorescence parameters, the forward-angle light scattering intensity (FALS) has been determined as an indicator of cell size. Comparing different temporal positions within the cell cycle, the determined FALS distributions show the lowest variability at the beginning of the S phase. The developed procedure in combination with multiparameter flow cytometry should be useful for studying the kinetics and regulation of the budding yeast cell cycle.

Bromodeoxyuridine↗

Role of the eNOS Glu298Asp variant on the GNB3825T allele dependent determination of alpha-adrenergic coronary constriction.

The 825T allele of a polymorphism at GNB3, encoding the G protein beta(3) subunit, is associated with an enhanced coronary blood flow (CBF) reduction in response to alpha(2)-, but not to alpha(1)-adrenoceptor activation. Because the regulation of vascular tone by alpha(2)-adrenoceptors includes direct vasoconstriction as well as vasodilatation by endothelial release of nitric oxide, the eNOS Glu298Asp variant might further contribute to explain the variability of CBF reduction in response to alpha-adrenoceptor activation. Genotyping at the GNB3 and the eNOS gene was performed on 48 individuals receiving either the alpha(1)-adrenoceptor agonist methoxamine (5 mg i.c.) and/or the alpha(2)-adrenoceptor agonist BHT 933 (5 mg i.c.). CBF was calculated from quantitative coronary angiography and intracoronary Doppler flow velocity measurement. To analyse the impact of genotypes and coronary artery disease, a linear regression model was used, including cholesterol levels, heart rate, smoking and mean aortic blood pressure. An initial, univariate analysis suggested an impact of the eNOS Glu298Asp variant on alpha(2)-adrenoceptor-induced coronary constriction (CBF reduction 53.4 ch006.1 TT/TG versus 30.7 ch006.9% GG; P = 0.003). However, multifactorial analysis showed that the GNB3825T allele was associated exclusively with the CBF reduction on alpha(2)-adrenoceptor activation (58.2 +/- 4.4% TT/TC versus 27.9 +/- 4.3% CC; P < 0.0001). Contrary to the initial analysis, the Glu298Asp variant of the eNOS gene provides no additional information on the genetic basis of alpha(2)-adrenoceptor-induced coronary vasoconstriction, which appears exclusively associated to the 825T allele at GNB3. Analysis of modifying genes appears crucial for the understanding of genetic associations.

Adrenergic alpha-Agonists↗

Genetic variability and genetic structure of wild and semi-domestic populations of tasar silkworm (Antheraea mylitta ) ecorace Daba as revealed through ISSR markers.

The genetic diversity in the wild and semi-domestic populations of Daba ecorace of Antheraea mylitta was studied to ascertain the distribution of variability within and among populations of semi-domestic bivoltine (DB), trivoltine (DT) and nature grown wild populations (DN) with inter-simple sequence repeat (ISSR) markers. A total of 138 markers were produced among 56 individuals of the three populations, of which 98% were polymorphic. For the individual populations, the percentage polymorphism was 58.69, 52.9 and 77.54 for DB, DT and DN, respectively. Average number of observed (1.791+/- 0.408) and effective alleles (1.389+/-0.348) was also high in the wild populations in comparison to the bivoltine and trivoltine semi-domestic populations. Genetic diversity (H(t)) in DB, DT and DN was 0.180+/- 0.033, 0.153+/- 0.032 and 0.235+/- 0.033, respectively and within-population genetic diversity (H(s)) ranged from 0.166 to 0.259 with a mean of 0.189. Mean gene differentiation (G(ST)) was found to be 0.25. Shanon's diversity index was 0.278, 0.237 and 0.361 for DB, DT and DN and overall it was 0.391. Gene flow (N(m)) among the populations was 1.509. The dendrogram produced by UPGMA with Dice's genetic distance matrices resulted in the formation of three major clusters separating the three populations. Considerable intra- and inter-population variability is found in all three populations. The population structure analysis further suggests that the semi-domestic populations of Daba ecorace are at the threshold of differentiating themselves. The high genetic variability present within wild Daba population of A. mylitta is of much importance for conservation as well as utilization in systematic breeding program.

Alleles↗

Selection at multiple checkpoints focuses V(H)12 B cell differentiation toward a single B-1 cell specificity.

Phosphatidyl choline (PtC)-specific B cells segregate to the B-1 subset, where they comprise up to 10% of the B-1 repertoire. About half express V(H)12 and Vkappa4/5H and are restricted in V(H)CDR3. We have previously reported that anti-PtC V(H)CDR3 is enriched among V(H)12-expressing cells by selective elimination of pre-B cells. We report here a bias for Vkappa4/5H expression among V(H)12-expressing B cells, even among those that do not bind PtC and are not B-1. This is due in part to an inability of V(H)12 to associate with many light (L) chains but must also be due to a selective advantage in survival or clonal expansion in the periphery for Vkappa4/5H-expressing cells. Thus, the bias for Vkappa4/5H expression is independent of PtC binding, and, as segregation to B-1 occurs after Ig gene expression, it precedes segregation to the B-1 subset. In 6-1 mice, splenic B-1 cells reside in follicles but segregate to follicles distinct from those that contain B-2 cells. These data indicate that selection at multiple developmental checkpoints ensures the co-expression of an anti-PtC V(H)CDR3 and L chain in a high frequency of V(H)12 B cells. This focus toward specificity for PtC facilitates the development of a large anti-PtC B-1 repertoire.

Amino Acid Sequence↗

A new recombinant single chain trispecific antibody recruits T lymphocytes to kill CEA (carcinoma embryonic antigen) positive tumor cells in vitro efficiently.

Anti-tumor associated antigen (TAA).CD3.CD28 trispecific antibody(TsAb) is able to provide two signals for fully and continuously activation of T lymphocytes and recruit them around tumor cells, presenting an attractive concept in tumor immunotherapy. Here, a new single chain trispecific antibody (scTsAb), named CEA-scTsAb, was constructed by fusion of anti-CEA (Carcinoma Embryonic Antigen) single chain antibody (scFv), anti-CD3 scFv and anti-CD28 VH, spaced by polypeptide interlinkers taken from the fragment of constant region (FC) of human IgG and human serum albumin (HSA). It was expressed in Escherichia coli at low temperature (30 degrees C) with up to 50% of the antibody being present in soluble form. After one step of DEAE anion chromatography, the soluble product was sufficiently pure for further in vitro activity assays. First, it was proved that CEA-scTsAb could recognize three antigens (CEA, CD28 and Jurkat cell membrane antigen) specifically and could distinguish antigen positive cells from antigen negative cells in vitro. Then fresh PBMC (peripheral blood mononuclear cells), without being pre-treated by co-stimulatory reagents, such as IL-2 or CD28 mAb, were used as effector cells to test their ability to mediate tumor specific cytolysis of CEA-positive tumor cells, SW1116. It was found by photomicrography that T lymphocytes were attracted to SW1116 cells in the presence of CEA-scTsAb, which resulted in effective cytolysis of tumor cells. As shown by MTT assay, the efficacy of tumor specific cytolysis mediated by CEA-scTsAb related to both the quantity and activation of PBMC. At an effector cells/target cells ratio (E/T) of 5, it was proved by dual-color FACS with propidium iodide (PI) and FITC-annexin V that both necrosis and apoptosis of tumor cells were causes of tumor specific cytolysis. In summary, a new single chain trispecific (CEA x CD3 x CD28) antibody was constructed and characterized carefully in this paper and was found to possess functions: (i) to activate T lymphocytes independently of additional co-stimulatory signal, (ii) to attract activated T lymphocytes around CEA-positive tumor cells, (iii) to attack CEA-positive tumor cells with recruited T lymphocytes. Because it recognizes a widely distributed tumor antigen (CEA), with moderate molecular weight (about 75 kDa) and a simple production procedure, and is able to mediate a high level of tumor specific cytolysis without any additional co-stimulating reagents, CEA-scTsAb is very promising for the task of immunotherapy in future.

Antibodies, Monoclonal↗