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Assignment of the human pulmonary surfactant protein D gene (SFTP4) to 10q22-q23 close to the surfactant protein A gene cluster.

Pulmonary surfactant consists of a complex mixture of phospholipids and several proteins essential to normal respiratory function. Two of the surfactant proteins, SP-A and SP-D, appear to have lectin-like activity relevant to the local phagocytic defense. Using polymerase chain reaction (PCR)-based somatic cell hybrid mapping, the human SP-D gene (SFTP4) was assigned to chromosome 10. A regional mapping panel was assembled and characterized using sequence tagged sites for five loci previously mapped to 10q. SFTP4, the SP-A gene (SFTP1), and the microsatellite D10S109 were placed in the interval 10q22-q23. Low-stringency PCR using the SFTP1 primer pair suggested the presence of at least two additional SP-A-related genes in the same region. With the locus for mannose-binding lectin (MBL) at 10q21, this may be indicative of this region's central role in the evolutionary history of carbohydrate-binding proteins containing collagen-like regions.

Animals↗

Maternal and paternal lineages of the Samaritan isolate: mutation rates and time to most recent common male ancestor.

The Samaritan community is a small, isolated, and highly endogamous group numbering some 650 members who have maintained extensive genealogical records for the past 13-15 generations. We performed mutation detection experiments on mitochondrial DNAs and Y chromosomes from confirmed maternal and paternal lineages to estimate mutation rates in these two haploid compartments of the genome. One hundred and twenty four DNA samples from different pedigrees (representing 200 generation links) were analyzed for the mtDNA hypervariable I and II regions, and 74 male samples (comprising 139 links) were typed for 12 Y-STRs mapping to the non-recombining portion of the Y chromosome (NRY). Excluding two somatic heteroplasmic substitutions and several length variants in the homopolymeric C run in the HVII region, no mutations were found in the Samaritans' maternal lineages. Based on mutations found in Samaritan paternal lineages, an estimate of a mutation rate of 0.42% (95% confidence interval of 0.22%-0.71%) across 12 Y-STRs was obtained. This estimate is slightly higher than those obtained in previous pedigree studies in other populations. The haplotypes identified in Samaritan paternal lineages that belong to the same haplogroup were used to estimate the number of generations elapsed since their most recent common ancestor (MRCA). The estimate of 80 generations corresponds with accepted traditions of the origin of this sect.

Biological Evolution↗

The MGEA6 multigene family has an active locus on 14q and at least nine pseudogenes on different chromosomes.

The meningioma expressed antigen-6 (MGEA6) was originally identified as an immunogenic antigen in meningioma patients. Somatic hybrid panel mapping and fluorescence in situ hybridization revealed MGEA6-related sequences on different human chromosomes. Here we carry out database analysis to investigate the complexity of the MGEA6-related sequences and demonstrate the existence of a multigene family. We localized the active gene (spanning over 83 kb) to chromosome 14q and elucidated its exon/intron structure. We identified and characterized 9 processed pseudogenes on 9 different chromosomes including chromosomes 2, 3, 6, 7, 9, 10, 12, 13, and 18. We performed phylogenetic analysis and concluded that the MGEA6 pseudogenes may result from more than one retrotransposition event; we calculated divergence times of the pseudogenes to be between 21.5 and 28.9 million years ago.

Alternative Splicing↗

Foxl2 function in ovarian development.

Foxl2 is a forkhead transcription factor essential for proper reproductive function in females. Human patients carrying mutations in the FOXL2 gene display blepharophimosis/ptosis/epicanthus inversus syndrome (BPES), an autosomal dominant disease associated with eyelid defects and premature ovarian failure in females. Recently, animal models for BPES have been developed that in combination with a catalogue of human FOXL2 mutations provide further insight into its molecular function. Mice homozygous mutant for Foxl2 display craniofacial malformations and female infertility. The analysis of the murine phenotype has revealed that Foxl2 is required for granulosa cell function. These ovarian somatic cells surround and nourish the oocyte and play an important role in follicle formation and activation. Mutations upstream of FOXL2 in humans, not affecting the coding sequence itself, have also been shown to cause BPES, which points to the existence of a distant regulatory element necessary for proper gene expression. The same regulatory sequences may be deleted in the goat polled intersex syndrome (PIS), in which FoxL2 expression is severely reduced. Sequence comparison of FoxL2 from several vertebrate species has shown that it is a highly conserved gene involved in ovary development. Thus, the detailed understanding of Foxl2 function and regulation and the identification of its transcriptional targets may open new avenues for the treatment of female infertility in the future.

Abnormalities, Multiple↗

Neuronal architecture in nucleus magnocellularis of the chicken auditory system with observations on nucleus laminaris: a light and electron microscope study.

This report presents the major structural features of neurons and their afferent input in nucleus magnocellularis, the avian homologue of the mammalian anteroventral cochlear nucleus. Results of light-microscope observations, as seen in Golgi, Nissl, and normal fiber preparations, as well as ultrastructural morphology are reported. In addition, cells and axons in nucleus laminaris, the presumed homologue of the mammalian medial superior olivary nucleus, are also described. In Golgi-impregnated material, the mature principal cell in nucleus magnocellularis has an ovoid soma encrusted with somatic spines. A dendrite, when present, emerges from the cell soma, travels for a short distance and breaks into a tuft of stubby terminal branches. Foremost among the afferents to nucleus magnocellularis are auditory nerve axons that terminate in large, axosomatic endings, or end-bulbs, covering a large portion of the somatic surface. Other afferents, which also end in relation to the perikaryon, are of undetermined and perhaps multiple origins. The neurons resemble the bushy cells of the mammalian anteroventral cochlear nucleus. Evidence is presented that individual axons from the nucleus magnocellularis bifurcate and send branches to the nucleus laminaris bilaterally, thus placing constraints on the binaural interactions possibly involved in lateralization functions. In electron micrographs, the end-bulbs appear as large, elongate structures which can cover a third of the cell soma. Multiple sites of synaptic specialization occur along these terminals. The synaptic membrane complexes may form directly on the cell body or on the sides or crests of somatic spines. These complexes are characterized by asymmetric membrane densities with a cluster of clear, spherical vesicles on the axonal side. Other small terminal profiles are also present on the somata receiving the end-bulbs. Dendritic profiles are scarce, in agreement with observations in Golgi impregnations. The structural findings indicate that the medial part of the nucleus magnocellularis is homologous to the anterior part of the mammalian anteroventral cochlear nucleus in that the neurons of nucleus magnocellularis are homologous to the bushy cells of the cat. On this basis, the cells in nucleus magnocellularis could faithfully preserve the acoustic response patterns generated in the auditory nerve. This should, in turn, allow a secure relay of bilateral latency differences essential for binaural interactions in the nucleus laminaris.

Animals↗

Identification of the activation-induced cytidine deaminase gene from zebrafish: an evolutionary analysis.

In the present study, we report the identification of the activation-induced cytidine deaminase (AID) encoding gene in frog, dog and chimpanzee, where both somatic hypermutation and class switch recombination (CSR) occurs and in zebrafish and fugu, species lacking CSR. The cDNA sequence of the zebrafish AID reported here suggests both N and C ends of the previously predicted protein sequence are incorrect. A comparison of AID sequences among mammals, birds, amphibians and fish revealed conserved aa residues which may be essential for AID activity, although the cytidine deaminase active motif in the latter is nine amino acids longer. Furthermore, an aa deletion, and extensive substitutions in the C terminal end of AID from bony fish indicate that the molecule may not yet have developed a capacity to recruit the specific cofactor(s) needed to initiate CSR.

Amino Acid Sequence↗

Genetic disorders and the ethical status of germ-line gene therapy.

Recombinant DNA technology will soon allow physicians an opportunity to carry out both somatic cell- and germ-line gene therapy. While somatic cell gene therapy raises no new ethical problems, gene therapy of gametes, fertilized eggs or early embryos does raise several novel concerns. The first issue discussed here relates to making a distinction between negative and positive eugenics; the second issue deals with the evolutionary consequences of lost genetic diversity. In distinguishing between positive and negative eugenics, the concept of malady is applied as a definitional criterion for identifying genetic disorders that could qualify for germ-line therapy. Because gene replacement techniques are currently unavailable for humans, and because even if they were possible the number of people involved would be quite small, the loss of diversity concern seems moot. Finally, we discuss the issue of iatrogenic disorders associated with gene therapy and discuss several 'real world considerations.'

Biological Evolution↗

Oogenesis in the viviparous matrotrophic lizard Mabuya brachypoda.

Oogenesis in the lizard Mabuya brachypoda is seasonal, with oogenesis initiated during May-June and ovulation occurring during July-August. This species ovulates an egg that is microlecithal, having very small yolk stores. The preovulatory oocyte attains a maximum diameter of 0.9-1.3 mm. Two elongated germinal beds, formed by germinal epithelia containing oogonia, early oocytes, and somatic cells, are found on the dorsal surface of each ovary. Although microlecithal eggs are ovulated in this species, oogenesis is characterized by both previtellogenic and vitellogenic stages. During early previtellogenesis, the nucleus of the oocyte contains lampbrush chromosomes, whereas the ooplasm stains lightly with a perinuclear yolk nucleus. During late previtellogenesis the ooplasm displays basophilic staining with fine granular material composed of irregularly distributed bundles of thin fibers. A well-defined zona pellucida is also observed. The granulosa, initially composed of a single layer of squamous cells during early previtellogenesis, becomes multilayered and polymorphic. As with other squamate reptiles, the granulosa at this stage is formed by three cell types: small, intermediate, and large or pyriform cells. As vitellogenesis progresses the oocyte displays abundant vacuoles and small, but scarce, yolk platelets at the periphery of the oocyte. The zona pellucida attains its maximum thickness during late oogenesis, a period when the granulosa is again reduced to a single layer of squamous cells. The vitellogenic process observed in M. brachypoda corresponds with the earliest vitellogenic stages seen in other viviparous lizard species with larger oocytes. The various species of the genus Mabuya provided us with important models to understand a major transition in the evolution of viviparity, the development of a microlecithal egg.

Animals↗

Structural analysis of the nurse shark (new) antigen receptor (NAR): molecular convergence of NAR and unusual mammalian immunoglobulins.

We recently have identified an antigen receptor in sharks called NAR (new or nurse shark antigen receptor) that is secreted by splenocytes but does not associate with Ig light (L) chains. The NAR variable (V) region undergoes high levels of somatic mutation and is equally divergent from both Ig and T cell receptors (TCR). Here we show by electron microscopy that NAR V regions, unlike those of conventional Ig and TCR, do not form dimers but rather are independent, flexible domains. This unusual feature is analogous to bona fide camelid IgG in which modifications of Ig heavy chain V (VH) sequences prevent dimer formation with L chains. NAR also displays a uniquely flexible constant (C) region. Sequence analysis and modeling show that there are only two types of expressed NAR genes, each having different combinations of noncanonical cysteine (Cys) residues in the V domains that likely form disulfide bonds to stabilize the single antigen-recognition unit. In one NAR class, rearrangement events result in mature genes encoding an even number of Cys (two or four) in complementarity-determining region 3 (CDR3), which is analogous to Cys codon expression in an unusual human diversity (D) segment family. The NAR CDR3 Cys generally are encoded by preferred reading frames of rearranging D segments, providing a clear design for use of preferred reading frame in antigen receptor D regions. These unusual characteristics shared by NAR and unconventional mammalian Ig are most likely the result of convergent evolution at the molecular level.

Amino Acid Sequence↗

From individual control to majority rule: extending transactional models of reproductive skew in animal societies.

Transactional concession models of social evolution explain the reproductive skew within groups by assuming that a dominant individual completely controls the allocation of reproduction to other group members. The models predict when the dominant will benefit from donating parcels of reproduction to other members in return for peaceful cooperation. Using linear programming methods, we present a 'majority-rules' model in which the summed actions of all society members, each with equal power, completely determine the reproductive share of any single member. The majority-rules model predicts that, despite the diffusion of power, a 'virtual dominant' (a dominant lacking special behavioural power) will emerge and that the reproductive skew will be exactly that predicted if the virtual dominant were to control completely the group's reproductive partitioning. The virtual dominant is the individual to which group members have the maximum average genetic relatedness. This result greatly broadens the applicability of transactional models of reproductive skew to social groups of any size, such as large-colony eusocial insects, and explains why queens in such colonies can achieve reproductive domination without any behavioural enforcement. Moreover, the majority-rules model unifies transactional-skew theory with models of worker policing and even generates a new theory for the cooperation among somatic cells in a multicellular organism.

Animals↗

Molecular phylogeny of the volvocine flagellates.

Phylogenetic studies of approximately 2,000 bases of sequence from the large and small nuclear-encoded ribosomal RNAs are used to investigate the origins of the genus Volvox. The colonial and multicellular genera currently placed in the family Volvocaceae form a monophyletic group that is significantly closer phylogenetically to Chlamydomonas reinhardtii than it is to the other unicellular green flagellates that were tested, including Chlamydomonas eugametos, Chlorella pyrenoidosa, and Haematococcus lacustris. Statistical analysis of 251 phylogenetically informative nucleotide positions rejects the "volvocine lineage" hypothesis, which postulates a monophyletic evolutionary progression from unicellular organisms (such as Chlamydomonas), through colonial organisms (e.g., Gonium, Pandorina, Eudorina, and Pleodorina) demonstrating increasing size, cell number, and tendency toward cellular differentiation, to multicellular organisms having fully differentiated somatic and reproductive cells (in the genus Volvox). The genus Volvox appears not to be monophyletic. Volvox capensis falls outside a lineage containing other representatives of Volvox (V. aureus, V. carteri, and V. obversus), and both of these Volvox lineages are more closely related to certain colonial genera than they are to each other. This implies either a diphyletic origin of Volvox from different colonial volvocacean ancestors, a phylogenetic derivation of some of the colonial genera from a multicellular (i.e., Volvox) ancestor, or both. Considered together with previously published observations, these results suggest that the different levels of organizational and developmental complexity found in the Volvocaceae represent alternative stable states, among which evolutionary transitions have occurred several times during the phylogenetic history of this group.

Animals↗

Somatic genetic changes in human breast cancer.

Quantitative imbalance in chromosomal material relative to the normal diploid situation is the most conspicuous genetic change in breast tumors, affecting virtually all chromosomes in varying frequencies. This imbalance is reflected by deviant DNA stemlines observed in DNA flow cytometry analysis, by numerical chromosome abnormalities in karyotype analysis and by loss of heterozygosity in DNA polymorphism studies. Gene amplification might be caused by the same genetic mechanisms that cause these chromosomal abnormalities [134]. The number of known genes for which there is now good evidence for their role in the development of breast cancer is still limited, and basically restricted to TP53 and ERBB2. Clearly, the estrogen receptor, not discussed here, can be conjectured to be of importance in breast cancer development, yet the significance of the reported sequence variants [157] for hormone-independent growth is presently undetermined [158]. For many others, such as MYC, CCND1, EMS1, EGF, RB1, NME, DCC and prohibitin, the evidence is still largely circumstantial, or obtained only by in vitro studies on breast cancer cell lines. In many cases of chromosomal imbalance and certainly those affecting whole chromosomes or chromosome arms, it is unclear what their effect on tumor growth will be, because multiple potential candidate genes are located in the affected region. In addition, it is obvious that multiple chromosomes are affected simultaneously in a single tumor, but that the total set of chromosome changes varies in different tumors. This intra- and intertumor heterogeneity of chromosome involvement suggests that an unknown number of the observed abnormalities are not important for tumor development, but merely result from genetic instability. On the other hand, there is accumulating evidence, particularly from flow cytometry and allelotype studies reviewed here, to suggest that the genetic evolution associated with tumor development and progression does reach a stage of equilibrium despite the presence of extensive tumor heterogeneity. The number of genetic events found per tumor raises the question whether each event of heterozygosity loss represents the second step in the inactivation of a tumor suppressor gene. Also, LOH observed with polymorphic markers can sometimes be interpreted as allelic copy number gain instead of loss. Possibly, some of these allelic imbalances contribute to the tumorigenic process simply because they create a dosage effect in certain gene products [2]. This supposes that the sole presence of allelic imbalance at certain chromosomes is sufficient to provide selective growth advantage in certain cases.(ABSTRACT TRUNCATED AT 400 WORDS)

Breast Neoplasms↗

Gonadal dimorphism explained as a dosage effect of a locus on the sex chromosomes, the gonad-differentiation locus (GDL).

In human somatic cells bearing two X chromosomes, one X is genetically inactivated throughout most of its length, whereas in cells with one X and one Y both sex chromosomes are active (with the exception of the constitutive heterochromatin of the Y that is inert). The vast base of information concerning normal and abnormal human sexual development that has accumulated since the advent of human cytogenetics 3 decades ago can be integrated by the following hypothesis: Homologous gonad-differentiation loci (GDLs) exist on the X and Y. The GDLs are strictly sex-linked; that is, normally they do not recombine during spermatogenesis, so that considerable divergence in DNA sequence doubtless has occurred between the locus on the X and the locus on the Y. The abundance of their evolutionarily conserved product--a substance still to be identified--determines the path of differentiation that the indifferent gonadal anlage of the early embryo will take: if only one GDL is transcribed, the case when two X chromosomes are present, ovary will develop; if two GDLs are transcribed, the case when a Y is present along with an X, testis will develop. By implication, facultative X inactivation is an integral and essential component of the system adopted in mammalian evolution for accomplishing gonadal--viz., sexual--dimorphism.

Chromosome Mapping↗

The influence of Weismann's germ-plasm theory on the distinction between learned and innate behavior.

Since the early twentieth century it has been common in both psychology and behavioral biology to draw a sharp distinction between learned and innate behavior, or elements of behavior. The persistence of this dichotomy may be attributed in part to the fundamental importance of the separation of inherited and acquired characters within neo-Darwinian evolutionary theory, one of the essential foundations for the modern study of behavior. A cornerstone of early neo-Darwinian thought was August Weismann's theory of the germ plasm, which proposed a segregation between germinal and somatic cells during development, thus ruling out the possibility that acquired characters could be inherited. This denial of Lamarckian hereditary mechanisms became one of the hallmarks of neo-Darwinism, as opposed to classical Darwinism. Within the neo-Darwinian framework it thus became important, as Weismann himself pointed out, to distinguish sharply between inherited and acquired characters. Although the dichotomy has frequently been criticized it remains tenacious, surfacing in different guises as older versions of it became terminologically unacceptable. The analysis offered here suggests that this tenacity may partly be explained by the implications of Weismann's germ-plasm theory, and its modern incarnation in the central dogma of molecular genetics, and by the central thematic position of those ideas in the neo-Darwinian foundations of modern behavioral biology.

Behavioral Sciences↗

[Evolutionarily-conserved gene CKAP2,located in region 13q14.3 of the human genome, is frequently rearranged in various tumors].

The human CKAP2 gene, which is involved in diffuse large B-cell lymphomas, was localized via screening the GeneBridge 4 somatic cell radiation hybrid panel by means of the polymerase chain reaction (PCR). The CKAP2 gene was mapped between the WI-15460 and WI-3673 markers at the boundary between regions 13q14.3 and 13q21.1, at the distance of 14.39 cR (with 4.8 cR per cM) from the WI-5867 framework marker (lod score > 2.26). The human CKAP2 gene displayed high homology to mouse and rat expressed orthologs, A CKAP2-like sequence was found in human chromosome 14 and assumed to be a pseudogene resulting from duplication and subsequent mutations of the CKAP2 gene on chromosome 13. A possible role of the CKAP2 gene in oncogenesis associated with deletions and rearrangements of region 13q14.3-21.1 is discussed.

Animals↗

The complete sequence of the murine monoclonal immunoglobulin MOPC 173 (IgG2a): genetic implications.

The complete amino acid sequence of the murine monoclonal immunoglobulin MOPC 173 (IgG2a, kappa) is reported. The heavy chain contains 447 amino-acid residues, and one carbohydrate prosthetic group attached to the ASX residue 299. The kappa light chain is composed of 214 residues. The H chains are covalently linked by 3 interchain disulfide bridges. The H-L bond-forming cysteine of the H chain is between the VH and the CH1 domain. Intrachain bridges are disposed linearly, according to the classical model. There is no simple relationship between the primary structure and any given function of a particular domain. This is presumably due to the fact that the selection pressure exerts itself on the three-dimensional structure which may retain a conserved general organization as a result of balanced multiple mutations. Selection seems to act in two ways: --horizontally, in a multigene system such as the immunoglobulin classes (C domains of the heavy chains), leading to interclass homologies which are particularly marked for all the COOH-terminal domains of H and L chains which have, in addition a fair degree of homology with human beta2 microglobulin (about 30% identities); --vertically, in which case strictly homologous domains appear extremely conserved between distinct animal species. Conservation of the VH domains seems just as high as conservation of the CH domains. The VH region contains 3 types of positions: invariant and subgroup characteristic ("framework") which may be accounted for by a rather small number of germ-line genes, and hypervariable for which the origin of diversity, somatic or germinal, cannot be decided from sequence data alone. Murine VK domains, although basically built according to the same pattern, show a much more marked polymorphism of the framework, which might necessitate a higher number of basic germ-line genes. Finally, a hypothetical model of the switch mechanism is proposed. Rotational symmetry regions can be deduced at the DNA level from the known amino acid sequences of the switch peptides for the three translocational systems: H, kappa and lambda. These would provide recognition signals for restriction-like enzymes such as those which operate in prokaryotes. An implication of this model is the definition of an exact limit between the V and the C regions of all immunoglobulin chains.

Amino Acid Sequence↗

Probing the W chromosome of the codling moth, Cydia pomonella, with sequences from microdissected sex chromatin.

The W chromosome of the codling moth, Cydia pomonella, like that of most Lepidoptera species, is heterochromatic and forms a female-specific sex chromatin body in somatic cells. We collected chromatin samples by laser microdissection from euchromatin and W-chromatin bodies. DNA from the samples was amplified by degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR) and used to prepare painting probes and start an analysis of the W-chromosome sequence composition. With fluorescence in situ hybridization (FISH), the euchromatin probe labelled all chromosomes, whereas the W-chromatin DNA proved to be a highly specific W-chromosome painting probe. For sequence analysis, DOP-PCR-generated DNA fragments were cloned, sequenced, and tested by Southern hybridization. We recovered single-copy and low-copy W-specific sequences, a sequence that was located only in the W and the Z chromosome, multi-copy sequences that were enriched in the W chromosome but occurred also elsewhere, and ubiquitous multi-copy sequences. Three of the multi-copy sequences were recognized as derived from hitherto unknown retrotransposons. The results show that our approach is feasible and that the W-chromosome composition of C. pomonella is not principally different from that of Bombyx mori or from that of Y chromosomes of several species with an XY sex-determining mechanism. The W chromosome has attracted repetitive sequences during evolution but also contains unique sequences.

Animals↗

Identification of RAPD markers, in situ DNA content and structural chromosomal diversity in some legumes of the mangrove flora of Orissa.

Randomly amplified polymorphic DNA (RAPD) markers, karyotypes and 4C DNA content were analyzed in five legume mangroves belonging to the sub-family Papilinoideae (Dalbergia spinosa, Derris heterophylla and D. indica) and Caesalpinioideae (Caesalpinia crista, Cynometra ramiflora) of the family Fabaceae to establish the genetic variability and phylogenetic affinities. Somatic chromosome numbers were reported for the first time in D. spinosa (2n = 20), C. ramiflora (2n = 26) and D. heterophylla (2n = 24) with reconfirmation of the somatic chromosome number in D. indica (2n = 22) and C. crista (2n = 24). Significant intergeneric and interspecific variation of 4C DNA content was observed and that varied from 8.970 pg in C. ramiflora to 28.730 pg in D. indica. From the RAPD analysis, the dendogram showed clustering of Caesalpinia crista and Cynomitra ramiflora into one group (81.80). In the second groups Derris indica and Derris heterophylla were more similar (83.10) than Dalbergia spinosa (85.80). Species-specific DNA markers (900 bp) obtained in D. spinosa from OPN15; 700 and 2000 bp in C. ramiflora from OPN4 and 400 and 800 bp in D. heterophylla and 500 bp DNA fragment in C. crista obtained from OPN-11 were found characteristic RAPD markers of these species. C. crista found more closer affinity to C. ramiflora of the sub-family Caesalpinioideae [genetic distance (1-F) = 0.847]. Derris indica showed closer genetic relation with D. heterophylla [genetic distance (1-F) = 0.856] than D. spinosa [genetic distance (1-F) = 0.876] where Derris and Dalbergia belongs to the sub-family Papilionoideae. By employing these markers the present study has helped to resolve the relationship between the taxonomically diverse leguminous mangroves and study their ability to coexist with mangroves that would shed light on the evolution of mangroves from terrestrial species.

Caesalpinia↗