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Patterns of connections from the striate cortex to cortical visual areas in superior temporal sulcus of macaque and middle temporal gyrus of owl monkey.

Double label-emulsion autoradiography has been used in rhesus monkeys to study cortico-cortical connections, arising from two separate sites of the striate cortex, and going in the same hemisphere into the cortex in the medial part of the posterior (or ventral) bank of the superior temporal sulcus (area STS). The projections from a single cortical locus are segregated into several patches of labeled terminals in layers III-IV, which form bands in consecutive sections. Fields of distribution of these bands from two sites of area 17 may completely overlap, when they arise from neighboring regions, or may partially overlap, when they arise from more separated regions. The latter show a retinotopical order in these connections and, consequently, of area STS itself: central visual field is lateral and ventral in STS to peripheral visual field, and upper visual field is ventral and medial to lower visual field. Connections from area 17 to area MT in owl monkey were analyzed in a comparative study. Results show that these connections are also highly segregated into bands, and that those arising in separate, but neighboring regions of 17, may greatly overlap in MT. The retinotopy of these connections was not studied, however. The similar divergent distribution of area 17 connections to STS and MT, and the similarity of the topography of STS connections and of the known retinotopy of area MT, are considered as elements of homologies between these areas. Functional implications of these divergent patterns of connections to these motion-sensitive areas (Zeki, '74), are considered.

Animals↗

The B cell compartment of two chicken lines divergently selected for antibody production: differences in structure and function.

In the present study differences in the B cell compartment of two chicken lines selected for either high (H) or low (L) antibody response to sheep red blood cells (SRBC) are investigated. In non-immunized chicks, flow cytometry revealed generally more circulating Ig+ leukocytes in the H line, while in the L line slightly more CD4+ and in week 5, more CD8+ cells were found. In the L line spleen more CD8+ were found and in the H line spleen more CD4+ cells. In week 6, half of the chicks were immunized. Both lines were similarly affected by immunization. Immunization reduced the percentages of the circulating T cell subpopulations, while Ig+ cells were enhanced, compared with non-immunized chicks. Histological determinations with specific mAbs on spleens of young, non-immunized chicks, showed large dense T cell areas in the L line, while in the H line more and larger germinal centres were found. In the H line, also, more B cells were found in the peri-ellipsoid lymphoid sheaths (PELS). No line differences in mononuclear phagocytes were found other than associated with line differences in numbers of PELS and germinal centres. After immunization with TNP-BSA, both higher numbers of TNP-specific antibody producing cells and higher levels of circulating antibody were found in the H line. Moreover, more TNP-specific plasma cells were found in non TNP-immunized H line chicks, than in the L line chicks. The H line had also higher ELISA-titers to KLH 5 days after immunization with KLH. Therefore it was concluded that selection for antibody response has affected the B cell compartment. The H line has relatively more B cells and the splenic structure of the H line differs from the L line, in the H line probably resulting in a more optimal organization for antibody response to T cell dependent antigens.

Adjuvants, Immunologic↗

Rat calpastatin has diverged primary sequence from other mammalian calpastatins but retains functionally important sequences.

Rat calpastatin was cloned for cDNA and sequenced. It comprises 603 amino acid residues and contains four repeats of approx. 140 amino acid residues, each of which has TIPPxYr sequence responsible for calpain-inhibitory activity. However, rat calpastatin has three deletions of 30-40 amino acid residues in the nonessential regions for the inhibitory activity, and consequently, the deduced molecular size is significantly smaller than those of other mammalian calpastatins.

Amino Acid Sequence↗

Divergent effects of human lymphokine derived oligopeptides on PMNLs function of young and aged healthy subjects.

The effects of low molecular weight lymphokine-derived oligopeptides (LK-OPs) on PMNLs effector functions and receptor mediated biochemical events were studied in the case of healthy young and aged subjects. In the case of young subjects the low mol. wt. LK-OPs stimulated the Fc gamma receptor-mediated effector functions of PMNLs, whereas an inhibition was observed in PMNLs of the elderly (extracellular cytotoxicity and intracellular killing). The underlying biochemical events, induced by low mol. wt. LK-OPs stimulation, were also investigated. In PMNLs of young subjects the oxidative metabolism was stimulated (enhanced O2 consumption, O2 and H2O2 production) by low mol. wt. LK-OPs, while in elderly subjects it was inhibited. The cyclic nucleotides regulating the Fc gamma receptor mediated effector functions and the oxygen radicals formation showed an altered dynamic response under low mol. wt. LK-OPs stimulation with aging i.e. the cGMP level could not be changed at all. Our results suggest that low mol. wt. LK-OPs induced inhibition of Fc gamma receptor mediated effector functions with aging could be partly explained by an altered post receptorial coupling switch and as a consequence the lymphokines could not play their role of immunomodulators further impairing the altered immune response with aging.

Adult↗

Mechanism exploration of divergent partial denitrification performance under tetracycline stress: Insights from functional gene, electron transport and molecular docking.

Nitrates and antibiotics like tetracycline (TC) coexist in wastewater and inhibit nitrite (NO₂--N) accumulation during partial denitrification (PD), restricting anammox coupling. A moving bed biofilm reactor (PD-MBBR) and a sequencing batch reactor (PD-SBR) were compared under TC stress (0-8 mg/L). The PD-MBBR proved more robust, sustaining a high nitrate transformation ratio (NTR) of 95.11% and ∼53% TC removal. Metagenomic sequencing, quantitative polymerase chain reaction (qPCR), and molecular docking revealed this tolerance stemmed from physical shielding and metabolic compensation. Carrier-attached growth promoted extracellular polymeric substances (EPS) overproduction, forming a dense barrier preventing TC from binding to key denitrifying enzymes. The biofilm maintained stable nitrate reductase (NAR) activity via high narG and napA gene abundances, while nitrite reductase (NIR) was inhibited, ensuring efficient NO₂--N accumulation. This was supported by hyperactivated electron transport chain components, with complex III relative abundance increasing 15.08% and peak enzymatic activity reaching 149.02%. While IntI1-mediated horizontal gene transfer fortified community defense, concentrated antibiotic resistance genes (ARGs) within the biofilm pose a secondary dissemination risk. Thus, PD-MBBR provides an efficient pretreatment strategy for anammox, though downstream ARGs management is warranted.

Denitrification↗

Sequence divergence of coiled coils--structural rods, myosin filament packing, and the extraordinary conservation of cohesins.

The amino acid sequences of the long, anti-parallel coiled coils of the cohesin subunits SMC1 and SMC3 are almost totally conserved in mammals. To understand this exceptional conservation more broadly, we analyzed amino acid sequence variation for several groups of coiled-coil proteins. Some long coiled coils, including giantin, NuMA, and Ndc80p/Nuf2p diverge approximately 20% from humans to rodents, suggesting they function as spacer rods, whose sequence divergence is constrained only by the need to maintain the coiled-coil structure. Other coiled coils such as skeletal muscle myosin, intermediate filaments, and the lamins diverge only 1-3%. We suggest that this sequence divergence is constrained by the extensive packing contacts over the entire surface of the coiled-coil. The coiled coils of SMC5/6 and SMC2/4 (condensin) are slightly more constrained than the presumed spacer rods, diverging 10-15%. Conversely, the coiled coils of SMC1/3 (cohesin) diverge only 0.0-1.0%. This extreme constraint suggests that the entire surface of the coiled coil is intimately involved in the mechanism of sister chromatid cohesion. Direct binding of the coiled coils to chromatin, or perhaps the need to avoid such binding, are two possible mechanisms. Finally, analysis of the heptad repeat shows that the a and d positions are more constrained in spacer rods, and the bcefg positions more constrained in skeletal muscle myosin.

Actins↗

Pregnancy-specific glycoprotein (PSG) in baboon (Papio hamadryas): family size, domain structure, and prediction of a functional region in primate PSGs.

Pregnancy-specific glycoprotein (PSG) constitutes a major component of serum of pregnant women and appears to be essential for a successful pregnancy. Its function is, however, still unknown. Because of the evolutionary divergence between human and rodent PSG, functional studies may require a primate animal model. We have characterized PSG transcripts in a baboon placenta cDNA library and analyzed baboon genomic DNA. The main PSG isoform had the domain structure N-A1-B2-C similar to the human type IIa isoform. The type I isoform (N-A1-A2-B2-C) was also expressed. Fifteen similar PSG genes were identified of which at least nine were simultaneously expressed in third trimester baboon placenta. Thus, the baboon PSG family was as complex as that of humans. Recombinant baboon PSG (isoform IIa) had a molecular weight of 38 kDa and reacted with antibodies against human PSG. Comparative analysis of 43 N-domain amino acid sequences of PSG from four species and nine primate carcinoembryonic antigen subgroup N domain sequences identified a number of residues in the GFCC'C" ss-sheet and FG loop that are probable candidates for PSG binding to its putative ligand.

Animals↗

Divergent correlations of circulating dehydroepiandrosterone sulfate and testosterone with insulin levels and insulin receptor binding.

We evaluated the insulin response to a standard oral glucose tolerance test (OGTT) and in vitro insulin binding to erythrocytes (RBC) in 26 women from 3 groups: Group NW, normal women (n = 11); Group DS, women (n = 9) with elevated serum DHEAS concentrations, greater than 400 micrograms/dl (greater than 10.84 mumol/L); and Group IR, women (n = 6) with elevated basal plasma insulin concentrations (IRI). There was a significant linear correlation between the area under the insulin response curve (IRI-AUC) and serum testosterone (T) (r = 0.78, p = 0.0001). Using stepwise multiple linear regression, IRI-AUC was characterized as a function of both serum T and DHEAS; positively with T and negatively with DHEAS. In vitro (n = 17), there was a positive correlation between RBC-insulin binding and serum DHEAS (r = 0.54, p = 0.029) and a negative correlation between RBC-binding and T (r = -0.57, p = 0.017). We conclude that DHEAS may enhance insulin binding and action and that DHEAS and T have divergent functional relationships with IRI. DHEAS and T may therefore exert opposing effects on insulin secretion and action.

Dehydroepiandrosterone↗

Evolution of human alpha 1-acid glycoprotein genes and surrounding Alu repeats.

There is a mosaic pattern of variation between the two tandemly arranged human alpha 1-acid glycoprotein genes. Both the synonymous and the nonsynonymous sites of exons 3 and 4 are more divergent than the rest of the gene, suggesting that they have had a different evolutionary history. Comparisons of the two gene sequences with rat AGP indicate that exons 3 and 4 of AGP2 have been evolving without functional constraint since their divergence from AGP1. It is proposed that the conserved region of the gene has been homogenized recently by gene conversion with the homologous regions of AGP1. The Alu sequences surrounding the genes appear to have been involved in both the gene duplication and the gene conversion events.

Animals↗

NEEDLY, a Pinus radiata ortholog of FLORICAULA/LEAFY genes, expressed in both reproductive and vegetative meristems.

The LEAFY/FLORICAULA genes from Arabidopsis and Antirrhinum are necessary for normal flower development and play a key role in diverse angiosperm species. A homologue of these flower meristem-identity genes, NEEDLY (NLY), has been identified in Pinus radiata. Although the NLY protein shares extensive sequence similarity with its angiosperm counterparts, it is lacking the proline-rich and acidic motifs thought to function as transcriptional activation domains. NLY already is expressed during vegetative development at least 5 years before the transition to the reproductive phase. Expression of NLY in transgenic Arabidopsis promotes floral fate, demonstrating that, despite its sequence divergence, NLY encodes a functional ortholog of the FLORICAULA/LEAFY genes of angiosperms. Expression of the LFY::NLY transgene can largely complement the defects in flower development caused by a severe lfy allele.

Amino Acid Sequence↗

Characterization of the Escherichia coli AaeAB efflux pump: a metabolic relief valve?

Treatment of Escherichia coli with p-hydroxybenzoic acid (pHBA) resulted in upregulation of yhcP, encoding a protein of the putative efflux protein family. Also upregulated were the adjacent genes yhcQ, encoding a protein of the membrane fusion protein family, and yhcR, encoding a small protein without a known or suggested function. The function of the upstream, divergently transcribed gene yhcS, encoding a regulatory protein of the LysR family, in regulating expression of yhcRQP was shown. Furthermore, it was demonstrated that several aromatic carboxylic acid compounds serve as inducers of yhcRQP expression. The efflux function encoded by yhcP was proven by the hypersensitivity to pHBA of a yhcP mutant strain. A yhcS mutant strain was also hypersensitive to pHBA. Expression of yhcQ and yhcP was necessary and sufficient for suppression of the pHBA hypersensitivity of the yhcS mutant. Only a few aromatic carboxylic acids of hundreds of diverse compounds tested were defined as substrates of the YhcQP efflux pump. Thus, we propose renaming yhcS, yhcR, yhcQ, and yhcP, to reflect their role in aromatic carboxylic acid efflux, to aaeR, aaeX, aaeA, and aaeB, respectively. The role of pHBA in normal E. coli metabolism and the highly regulated expression of the AaeAB efflux system suggests that the physiological role may be as a "metabolic relief valve" to alleviate toxic effects of imbalanced metabolism.

Biological Transport↗

Organizational analysis of elav gene and functional analysis of ELAV protein of Drosophila melanogaster and Drosophila virilis.

Drosophila virilis genomic DNA corresponding to the D. melanogaster embryonic lethal abnormal visual system (elav) locus was cloned. DNA sequence analysis of a 3.8-kb genomic piece allowed identification of (i) an open reading frame (ORF) with striking homology to the previously identified D. melanogaster ORF and (ii) conserved sequence elements of possible regulatory relevance within and flanking the second intron. Conceptual translation of the D. virilis ORF predicts a 519-amino-acid-long ribonucleoprotein consensus sequence-type protein. Similar to D. melanogaster ELAV protein, it contains three tandem RNA-binding domains and an alanine/glutamine-rich amino-terminal region. The sequence throughout the RNA-binding domains, comprising the carboxy-terminal 346 amino acids, shows an extraordinary 100% identity at the amino acid level, indicating a strong structural constraint for this functional domain. The amino-terminal region is 36 amino acids longer in D. virilis, and the conservation is 66%. In in vivo functional tests, the D. virilis ORF was indistinguishable from the D. melanogaster ORF. Furthermore, a D. melanogaster ORF encoding an ELAV protein with a 40-amino-acid deletion within the alanine/glutamine-rich region was also able to supply elav function in vivo. Thus, the divergence of the amino-terminal region of the ELAV protein reflects lowered functional constraint rather than species-specific functional specification.

Amino Acid Sequence↗

Comparative sequence analysis as an approach to evaluating structure, function, and evolution of 5S and 5.8S ribosomal RNAs.

Nucleotide sequences of nine eukaryotic and nine eubacterial 5S rRNAs have been selected for their diversity and subjected to analysis of primary and potential secondary structure. This analysis has allowed the quantitative confirmation of several previously made observations concerning 5S rRNA structure: (i) these two 5S rRNAs are derived from a common ancestor and probably perform essentially the same function in protein synthesis; (ii) one domain of 5S rRNA has undergone considerable divergence of structure (and presumably function) since the separation of the eukaryotic and eubacterial lineages; and (iii) single-stranded regions are more highly conserved than double-stranded regions. In addition, this analysis leads us to propose that (i) some of the highly conserved nucleotide residues in single-stranded regions interact in a specific manner with protein components of the translational apparatus, and (ii) repetitive folding and unfolding of helical regions occurs in two regions of eukaryotic 5S rRNA and one region of eubacterial 5S rRNA. In the context of these observations and propositions we also consider the potential secondary structure of plant mitochondrial 5S rRNA. Nucleotide sequences of 5.85 rRNAs have yielded less information about secondary structure and possible functional interactions. However, we have identified highly conserved and variable regions within this molecule and we show (in contrast to the situation with 5S rRNA) that these do not correlate well with proposed single-stranded and helical regions in a current model of 5.8S secondary structure.

Animals↗

Diverged 5s rRNA sequences adjacent to 5s rRNA genes in the rDNA of Pythium pachycaule.

The non-transcribed spacer of the ribosomal DNA repeat of Pythium pachycaule was found to exist in two versions, one about 200 bp longer than the other. Both versions contained a conserved 5s rRNA gene in inverted orientation and a diverged copy of the 5s sequence as a tandem repeat, with a spacer of about 180 bp between them. This is the first report of multiple 5s-like sequences in the non-transcribed spacer of the rDNA of any organism. The two diverged 5s sequences differ from each other at nine positions in the 5' half of the sequence, but they have the same central 10-bp deletion and their 3' halves are identical. The diverged sequences, 5s' and 5s'', when aligned with the 5s sequence, have the same base at 63.9 and 58.8% of the positions respectively. The spacers between 5s sequences in both versions were highly conserved. The secondary structures of potential rRNA products of the diverged 5s sequences indicate that they may be pseudogenes. The relationships between the functional 5s gene and the diverged gene copies suggest that the 5s sequence family of P. pachycaule originated by duplication of an ancestral gene, followed by divergence and the introduction of heterogeneity. This work shows the potential for tandemization of 5s genes in the NTS, and may shed light on the evolutionary events that led to the transition from the rDNA-linked 5s genes found in Pythium species with filamentous zoosporangia to the unlinked tandem arrays found in Pythium species with globose zoosporangia.

Base Sequence↗

GAL1-GAL10 divergent promoter region of Saccharomyces cerevisiae contains negative control elements in addition to functionally separate and possibly overlapping upstream activating sequences.

The upstream activating sequence (UASG) of the adjacent and divergently transcribed GAL1 and GAL10 promoters of Saccharomyces cerevisiae regulates the induction of the corresponding genes in response to the presence of galactose. We constructed chimeric yeast promoters in which a different UAS, UASC from the iso-1-cytochrome c (CYC1) gene of S. cerevisiae, was fused at different locations upstream of GAL1 (UASC-GAL1 promoters) or GAL10 (UASC-GAL10 promoters) and used to monitor the activity of UASG in cells grown in the presence or absence of galactose. Though the CYC1 promoter is fully induced in yeast grown in glycerol medium, UASC-GAL chimeric promoters containing UASG were repressed as much as 400-fold (UASC-GAL1) or 1350-fold (UASC-GAL10) in this growth medium. Several distinct portions of the GAL1-GAL10 divergent promoter region blocked the UASC-induced expression of the GAL1 and GAL10 promoters, whereas others did not, suggesting that several distinct negative control elements are present that may repress transcription of GAL1 and GAL10 in the absence of galactose. The approximate locations of these negative control elements were delimited to sites adjacent to or possibly overlapping the sites at which the positive control protein GAL4 binds in UASG. Deletion derivatives of GAL4 that fail to induce transcription from the wild-type GAL promoters but retain the DNA binding domain significantly derepressed the expression of the UASC-GAL chimeric promoters. These results, combined with those of earlier studies, suggest the possibility that GAL4 normally induces transcription of GAL1 and GAL10 by blocking the activity of these negative control elements, in addition to stimulating transcription by a mechanism of positive control.

Chromosome Mapping↗

Highly diverged homologs of Saccharomyces cerevisiae mitochondrial mRNA-specific translational activators have orthologous functions in other budding yeasts.

Translation of mitochondrially coded mRNAs in Saccharomyces cerevisiae depends on membrane-bound mRNA-specific activator proteins, whose targets lie in the mRNA 5'-untranslated leaders (5'-UTLs). In at least some cases, the activators function to localize translation of hydrophobic proteins on the inner membrane and are rate limiting for gene expression. We searched unsuccessfully in divergent budding yeasts for orthologs of the COX2- and COX3-specific translational activator genes, PET111, PET54, PET122, and PET494, by direct complementation. However, by screening for complementation of mutations in genes adjacent to the PET genes in S. cerevisiae, we obtained chromosomal segments containing highly diverged homologs of PET111 and PET122 from Saccharomyces kluyveri and of PET111 from Kluyveromyces lactis. All three of these genes failed to function in S. cerevisiae. We also found that the 5'-UTLs of the COX2 and COX3 mRNAs of S. kluyveri and K. lactis have little similarity to each other or to those of S. cerevisiae. To determine whether the PET111 and PET122 homologs carry out orthologous functions, we deleted them from the S. kluyveri genome and deleted PET111 from the K. lactis genome. The pet111 mutations in both species prevented COX2 translation, and the S. kluyveri pet122 mutation prevented COX3 translation. Thus, while the sequences of these translational activator proteins and their 5'-UTL targets are highly diverged, their mRNA-specific functions are orthologous.

5' Untranslated Regions↗

TRPC3: a versatile transducer molecule that serves integration and diversification of cellular signals.

Transient receptor potential (TRP) proteins have been recognized as sensors for a wide variety of external and internal signals involved in maintenance of cellular homeostasis and control of physiological functions. Evidence of a striking versatility in terms of signal integration and transduction has been reported for members of the canonical (or classical) TRP subfamily (TRPCs). TRPC species are cation channel subunits and emerge as multifunctional signal transduction molecules that are able to function as components of divergent signalplexes. Results obtained in heterologous expression systems suggest TRPC3 as a paradigm of multifunctional signal transduction by a cation channel protein. TRPC3 serves cellular Ca(2+) signaling by multiple mechanisms and may control a variety of distinct physiological functions. In this review, we summarize current knowledge on the properties and possible signaling partners of TRPC3, and discuss the role of TRPC3 channel proteins in cellular signaling networks.

Animals↗

A genomic comparison of faster-sex, faster-X, and faster-male evolution between Drosophila melanogaster and Drosophila pseudoobscura.

A genomic comparison of Drosophila melanogaster and Drosophila pseudoobscura provides a unique opportunity to investigate factors involved in sequence divergence. The chromosomal arrangements of these species include an autosomal segment in D. melanogaster which is homologous to part of the X chromosome in D. pseudoobscura. Using orthologues to calculate rates of nonsynonymous (d(N)) substitutions, we found genes on the X chromosome to be significantly more diverged than those on the autosomes, but it is not true for segment 3L-XR which is autosomal in D. melanogaster (3L) and X-linked in D. pseudoobscura (XR). We also found that the median d(N) values for genes having reproductive functions in either the male, the female, or both sexes are higher than those for sequences without reproductive function and even higher for sequences involved in male-specific function. These estimates of divergence for male sex-related sequences are most likely underestimates, as the very rapidly evolving reproductive genes would tend to lose homology sooner and thus not be included in the comparison of orthologues. We also noticed a high proportion of male reproductive genes among the othologous genes with the highest rates of d(N). Reproductive genes with and without an orthologue in D. pseudoobscura were compared among D. melanogaster, D. simulans, and D. yakuba and it was found that there were in fact higher rates of divergence in the group without a D. pseudoobscura orthologue. These results, from widely separated taxa, bolster the thesis that sexual system genes experience accelerated rates of change in comparison to nonsexual genes in evolution and speciation.

Animals↗