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Results for “sequencing libraries”

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PubMed1991

Human interferon omega 1: isolation of the gene, expression in Chinese hamster ovary cells and characterization of the recombinant protein.

A gene encoding human interferon omega-1 (IFN-omega 1) was isolated from a cosmid library, sequenced and expressed in Chinese hamster ovary (CHO) cells under the control of an SV40-derived promoter/enhancer sequence. Culture supernatants of stably transfected cell clones contained biologically active IFN-omega 1 at concentrations up to 10 micrograms/l. Amplification of the expression vector containing a dhfr gene under methotrexate selection pressure resulted in yields up to 200 micrograms/l. Production of IFN-omega 1 was further enhanced 2- to 3-fold by propagation of the cells in the presence of n-butyrate. IFN-omega 1 was purified from culture supernatants by monoclonal antibody affinity chromatography. The resulting protein was at least 95% pure as determined by reverse-phase HPLC and size-exclusion HPLC. Sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE) showed two bands of about the same intensity with apparent molecular masses of 24.5 and 22.5 kDa. Upon treatment with peptide:N-glycosidase F, both bands were shifted to lower molecular masses (20.5 and 18.5 kDa), indicating that CHO cell-derived IFN-omega 1 is glycosylated; Asn-78 was identified as the glycosylation site. Analysis of the carbohydrate moiety using glycosidases and lectins revealed the presence of biantennary complex oligosaccharides containing neuraminic acid. Amino acid sequencing showed that only about 40% of the molecules have the expected N-terminus, whereas the others carry two additional amino acids derived from the signal sequence. C-terminal amino acid sequencing using carboxypeptidase P demonstrated that the smaller form of the protein lacks nine amino acids. Disulfide bridges were shown to connect Cys residues 1 and 99 as well as 29 and 139, respectively, as in IFN-alpha. The specific antiviral activity of recombinant, glycosylated human IFN-omega 1 on human cells was 2.6 x 10(8) IU/mg, not significantly different from that of the authentic, human leukocyte-derived protein.

Amino Acid Sequence↗

PubMed1992

Isolation and characterization of cDNA clones encoding the skeletal and smooth muscle Xenopus laevis beta tropomyosin isoforms.

cDNAs clones corresponding to the skeletal and smooth muscle beta tropomyosins isoforms were isolated from a Xenopus laevis embryo cDNA library. Sequence analysis indicated that the two isoforms are coded by a single gene that uses two couples of alternative exons. The expression of the X. laevis beta tropomyosin gene closely resembles that of the mammalian gene but differs from the avian gene.

Amino Acid Sequence↗

PubMedDate not supplied

The spoIIN279(ts) mutation affects the FtsA protein of Bacillus subtilis.

The spo-279(ts) mutation, originally thought to be located in the spoIIG operon of Bacillus subtilis, has been mapped in close proximity but outside of the spoIIG locus. This mutation defines a new gene, spoIIN, located midway between the spoIIG and the spoVE loci, and whose product is required for successful completion of the asymmetric septation step. The spoIIN locus was cloned using a combination of 'walking steps' upstream from the spoIIG region and hybridization screening of a bacteriophage lambda library. Sequencing of DNA fragments able to rescue the spoIIN279(ts) mutation revealed that the spoIIN locus is identical with the B subtilis counterpart of the Escherichia coli ftsA gene. After cloning the ftsA region from a strain containing the spoIIN279(ts) mutation we found that this mutation converts the ninth residue of the FtsA protein from serine to asparagine. The spoIIN279(ts) mutation, which is recessive, leads to filamentation during growth at 42 degrees C and causes defective formation of the sporulation septum at this non-permissive temperature. The FtsA protein is therefore required for proper cell septation, both during vegetative growth and sporulation. Possible additional roles of FtsA during sporulation are discussed.

Bacillus subtilis↗

PubMed1989

Cloning and analysis of a human 86-kDa heat-shock-protein-encoding gene.

An 86-kDa heat-shock-protein-encoding (hsp86) cDNA probe permitted to identify, in whole genomic human DNA, two EcoRI fragments of 2.6 and 5.3 kb. These two fragments, as well as an homologous phage lambda VIII1 harboring about 19 kb of human DNA, were isolated from genomic libraries. Sequence analysis revealed that three different genomic hsp86 sequences had been cloned, one of them being the 5' half of a functional gene. This gene contains several introns, as compared to the entire Hsp86-encoding sequence found in lambda VIII1, which represents a processed pseudogene. Cloned hsp86 promoter, with its TATA-box and a heat-shock element upstream at nt positions -25 and -75, respectively, was functional, as verified by fusion to the bacterial chloramphenicol acetyltransferase-encoding gene and its transient expression in vivo. The typical hsp86-type heat-shock regulation was observed, i.e., significant basal activity associated with an inducibility at elevated temperatures. Furthermore, accurate and efficient in vitro transcription was initiated at this hsp86 promoter, resulting in expression of the hsp86 gene, as well as the unrelated sequences.

Amino Acid Sequence↗

PubMed1989

Isolation and chromosomal localization of the human En-2 gene.

By low stringency hybridization we have isolated from a human cosmid genomic library sequences homologous with a probe from the Drosophila engrailed gene. Partial nucleotide sequence analysis shows a consensus splice acceptor site followed by an open reading frame (ORF) that can encode 104 amino acids; the first 94 amino acids have 71% identity with the Drosophila engrailed protein. The shared region contains a homeo domain and is within the region of engrailed shared with the Drosophila invected gene and the mouse En-1 and En-2 genes. At the amino acid level, the human sequence is 85% identical with the mouse En-1 gene and 100% identical with the mouse En-2 gene. Hybridization against a panel of human-hamster somatic cell hybrids maps this human En-2 gene to chromosome 7, and regional mapping by in situ hybridization to human chromosomes localizes it to region 7q36 at the end of the long arm.

Amino Acid Sequence↗

PubMed2026

CRISPGen: A deep generative framework for multi-objective CRISPR/Cas9 guide RNA design via Conditional Latent Diffusion and Dual-Critic Reinforcement Learning.

MOTIVATION: The CRISPR-Cas9 system offers transformative potential for precision genome editing, yet its clinical translation remains constrained by the risk of unintended off-target double-strand breaks. While current discriminative models excel at evaluating pre-specified candidate guides, resolving the fundamental antagonism between on-target cleavage efficiency and off-target specificity within a fixed sequence search space remains a major challenge. RESULTS: We present CRISPGen, a unified deep generative framework that reframes sgRNA design as a multi-objective constrained sequence synthesis problem. It integrates (i) DNABERT-2 genomic-language embeddings, (ii) a conditional latent diffusion generator conditioned on a user-specified on-target efficiency target, and (iii) a dual-critic reinforcement-learning (RL) stage that couples a frozen on-target efficiency critic with a cross-attention off-target discriminator (validation Pearson R=0.8157) trained on a unified corpus of experimental off-target events from six detection platforms. Across 1000 generated sgRNAs, CRISPGen reduces the mean off-target discriminator score by 99.7% relative to the pre-RL baseline and, under an exhaustive whole-genome screen of all 302,631,056 NGG PAM sites in GRCh38, yields zero perfect-match and only 55 one-mismatch genomic hits. We further show, transparently, that the internal on-target critic saturates under RL optimization - an instance of Goodhart's Law - and therefore assess on-target viability using an independent external CRISPRon screen (mean 47.10/100). Repeating the RL fine-tuning stage under three random seeds (with the diffusion generator, DNABERT-2 embeddings, and off-target discriminator held fixed) yields a stable operating point across seeds. Full diversity, per-mismatch, and reproducibility statistics are reported in the Results. AVAILABILITY: Source code is available at https://github.com/malekpouri/CRISPGen; the pre-trained checkpoints and the 3,000,000-sequence library are hosted on Hugging Face (https://huggingface.co/malekpouri/CRISPGen-Checkpoints) and archived on Zenodo under DOI 10.5281/zenodo.21428641.

CRISPR-Cas9↗

PubMed2026

Integrative dual-track transcriptomics reveals stage-specific coordination, regulatory divergence, and HSP90AA1-associated remodeling in human folliculogenesis.

Human folliculogenesis depends on coordinated yet non-identical developmental remodeling in the oocyte and its surrounding granulosa cells. When these two compartments remain synchronized and when they diverge into lineage-specific regulatory states, however, remains incompletely resolved. Here we performed an integrative dual-track re-analysis of the human RNA-seq dataset GSE107746, modeling oocytes and granulosa cells as distinct but developmentally linked compartments across follicular progression. Analysis of 148 sequencing libraries showed that compartment identity was the dominant source of transcriptomic variation, supporting compartment-aware downstream interpretation. Within this framework, oocytes followed a relatively continuous developmental trajectory, with substantial transcriptional remodeling already evident across adjacent stages, whereas granulosa cells showed weaker early-stage contrasts but markedly stronger late-stage reorganization, particularly around the antral and preovulatory transitions. Functional enrichment indicated that oocyte maturation was associated with RNA-processing and broader genome-regulatory remodeling, whereas granulosa maturation was dominated by progressive mitochondrial and bioenergetic activation. Co-expression analysis showed that both compartments contained strong late-stage programmes together with inverse early-state modules, indicating a shared systems-level architecture of maturation, although the hub-gene composition and biological content of these programmes were largely compartment-specific. Machine-learning validation reinforced this asymmetry: oocyte stage classification was best recovered from a compact eigengene-based representation, whereas granulosa stage discrimination was better resolved by a broader differential-expression-derived feature set. At the gene level, HSP90AA1 emerged as a stage-associated marker with compartment-specific behavior, showing progressive attenuation across oocyte development, assignment to the selected oocyte blue module, and sharper transitional dynamics in granulosa cells. Together, these findings support a model in which human folliculogenesis proceeds through coordinated but non-equivalent transcriptomic remodeling, with shared developmental logic at the systems level but distinct molecular execution in germline and somatic compartments.

Co-expression networks↗

PubMed1992

Structure of the mouse activin receptor type II gene.

Knowledge of the structures of the activin receptor genes is crucial to our understanding of the role of the activins, inhibins, and their receptors in developmental and physiological processes. The type II activin receptor (ActRc) has been shown to be a transmembrane protein with putative serine/threonine kinase activity. Using a human ActRc type II cDNA as a probe, 18 overlapping lambda clones containing portions of the mouse ActRc type II gene were isolated from a mouse 129SvE genomic library. Sequence analysis of the exons, exon-intron boundaries, and 5' and 3' non-translated regions as well as Southern blot analysis of mouse genomic DNA were used to establish the structure of the mouse ActRc type II gene. The mouse ActRc type II gene is encoded by 11 exons and spans greater than 66 kilobases. Two large introns (introns 1 and 4) contribute the majority of the gene size and are found to delineate exons which encode important domains of the activin receptor. Analysis of the 5' region of the gene reveals several putative transcription factor binding sites which may be important for the complex transcriptional regulation of this gene.

Activin Receptors↗

PubMed1986

Isolation and characterization of a novel cytochrome P-450-like pseudogene.

A rabbit liver P-450-like pseudogene has been isolated from a lambda phage genomic library. Sequence analysis revealed structural homology with respect to the rat P-450b and P-450e genes as well as a similar intron-exon organization. A 5'-proximal TATA box-like sequence and two 3'-distal putative polyadenylation signals were identified, and all putative intron-exon boundaries except at the 3'-splice site of intron 2 were found to follow the GT/AG rule. With allowance for apparent deletions and insertions, the structural homology of the amino acid sequence deduced from the pseudogene with respect to rabbit P-450 isozyme 2 is lower for exons 1 through 4 (18-28%) than for exons 5 through 9 (42-65%). S1 nuclease mapping showed that mRNAs complementary to the DNA sequence of exon 9 are expressed. However, due to the alterations in the pseudogene, it appears that functional P-450 would not be produced from such mRNAs.

Amino Acid Sequence↗

PubMed1989

Olfactory-specific cytochrome P-450. cDNA cloning of a novel neuroepithelial enzyme possibly involved in chemoreception.

We isolated cDNA clones for cytochrome P-450 genes expressed in the olfactory neuroepithelium by screening a corresponding rat cDNA library. Sequence analysis and RNA blot hybridization revealed a new cytochrome P-450, designated cytochrome P-450olf1, which is the first reported cytochrome P-450 mRNA uniquely expressed in the chemosensory organ. Cytochrome P-450olf1 shows intermediate level of sequence similarity (38-53% identity) to several liver cytochrome P-450 enzymes, suggesting that it belongs to the cytochrome P-450II family, but defines a new subfamily (cytochrome P-450IIG) within it. Cytochrome P-450II enzymes are known to process diverse organic compounds, including odorants. This, together with the specificity of cytochrome P-450olf1 to the sensory neuroepithelium, may indicate a role for this protein in olfactory reception.

Amino Acid Sequence↗

PubMed1988

The melanoma progression-associated antigen P3.58 is identical to the intercellular adhesion molecule, ICAM-1.

The 89kd cell surface glycoprotein, P3.58, is expressed on human malignant melanomas in situ where it is associated with an increased risk of metastatic disease. Monoclonal antibodies detecting denatured P3.58 were produced and used to isolate a P3.58 encoding cDNA clone from a human melanoma lambda expression library. Sequencing of the cDNA revealed that the P3.58 antigen is identical to the leukocyte intercellular adhesion molecule 1 (ICAM-1).

Amino Acid Sequence↗

PubMed1992

Mapping of a human brain voltage-gated calcium channel to human chromosome 12p13-pter.

Degenerate DNA oligomers coding for highly conserved regions of the voltage-gated calcium channel were synthesized for the polymerase chain reaction (PCR) using DNA from a human brain cDNA library as template. PCR amplified a 640-bp DNA fragment from the human brain cDNA library. Sequencing revealed that this fragment encodes part of a protein highly homologous to a subtype of the dihydropyridine-sensitive calcium channel cloned from rabbit heart and rat brain. Southern analysis of panels of somatic cell hybrids mapped the 640-bp fragment, CACNL1A1, to human chromosome 12p13-pter.

Amino Acid Sequence↗

PubMed1987

Molecular cloning of cDNAs encoding two isoforms of the catalytic subunit of protein phosphatase 2A.

Clones coding for the catalytic subunit of one of the major protein phosphatases (type 2A) were isolated from a porcine cDNA library. Sequence analysis indicated that two different mRNA species coded for this enzyme. The deduced amino acid sequences of the two forms (alpha and beta) of the enzyme were 98% identical and showed 95% identity with the partial sequence of the rabbit enzyme determined by amino acid sequencing. The use of specific oligonucleotide probes indicated that the mRNAs coding for the alpha and beta forms were about 2 kilobases in length, present in equal amounts in a porcine cell line (LLC-PK1), and were the products of two distinct genes. Southern analysis using the coding region of the alpha phosphatase cDNA as a probe suggested the existence of additional related phosphatase genes.

Amino Acid Sequence↗

PubMed1987

Cloning and tissue distribution of rat heart fatty acid binding protein mRNA: identical forms in heart and skeletal muscle.

A fatty acid binding protein (FABP) has been identified and characterized in rat heart, but the function and regulation of this protein are unclear. In this study the cDNA for rat heart FABP was cloned from a lambda gt11 library. Sequencing of the cDNA showed an open reading frame coding for a protein with 133 amino acids and a calculated size of 14776 daltons. Several differences were found between the sequence determined from the cDNA and that reported previously by protein sequencing techniques. Northern blot analysis using rat heart FABP cDNA as a probe established the presence of an abundant mRNA in rat heart about 0.85 kilobases in length. This mRNA was detected, but was not abundant, in fetal heart tissue. Tissue distribution studies showed a similar mRNA species in red, but not white, skeletal muscle. In general, the mRNA tissue distribution was similar to that of the protein detected by Western immunoblot analysis, suggesting that heart FABP expression may be regulated at the transcriptional level. S1 nuclease mapping studies confirmed that the mRNA hybridized to rat heart FABP cDNA was identical in heart and red skeletal muscle throughout the entire open reading frame. The structural differences between heart FABP and other members of this multigene family may be related to the functional requirements of oxidative muscle for fatty acids as a fuel source.

Amino Acid Sequence↗

PubMed2024

Transcriptomic pathology of neocortical microcircuit cell types across psychiatric disorders.

Psychiatric disorders such as major depressive disorder (MDD), bipolar disorder (BD), and schizophrenia (SCZ) are characterized by altered cognition and mood, brain functions that depend on information processing by cortical microcircuits. We hypothesized that psychiatric disorders would display cell type-specific transcriptional alterations in neuronal subpopulations that make up cortical microcircuits: excitatory pyramidal (PYR) neurons and vasoactive intestinal peptide- (VIP), somatostatin- (SST), and parvalbumin- (PVALB) expressing inhibitory interneurons. Using laser capture microdissection followed by RNA sequencing (LCM-seq), we performed cell type-specific molecular profiling of subgenual anterior cingulate cortex, a region implicated in mood and cognitive control. We sequenced libraries from 130 whole cells pooled per neuronal subtype (VIP, SST, PVALB, superficial and deep PYR) in 76 subjects from the University of Pittsburgh Brain Tissue Donation Program, evenly split between MDD, BD and SCZ subjects and healthy controls (totaling 380 bulk transcriptomes from ~50,000 neurons). We identified hundreds of differentially expressed (DE) genes and biological pathways across disorders and neuronal subtypes, with the vast majority in interneurons, particularly PVALB. While DE genes were unique to each cell type, there was a partial overlap across disorders for genes involved in the formation and maintenance of neuronal circuits. We observed coordinated alterations in biological pathways between select pairs of microcircuit cell types, also partially shared across disorders. Finally, DE genes coincided with known risk variants from psychiatric genome-wide association studies, suggesting cell type-specific convergence between genetic and transcriptomic risk for psychiatric disorders. Our study suggests transdiagnostic cortical microcircuit pathology in SCZ, BD, and MDD and sets the stage for larger-scale studies investigating how cell circuit-based changes contribute to shared psychiatric risk.

Humans↗

PubMed1988

Multiple biological activities are expressed by a mouse interleukin 6 cDNA clone isolated from bone marrow stromal cells.

Interleukin 6 (IL-6) refers to the gene product that was characterized initially as beta 2 interferon/26-kDa protein produced by human fibroblasts and later was found to be identical to B-cell stimulatory factor 2, hybridoma/plasmacytoma growth factor, and probably hepatocyte-stimulating factor. Using the human IL-6 cDNA as a probe, we have isolated functional cDNA clones from mouse bone marrow stromal cell cDNA libraries. Sequence analysis of the mouse cDNA insert revealed significant homology between the human and mouse IL-6 cDNA clones both at the level of nucleotide (65%) and deduced amino acid (41%) sequences. The NH2-terminal sequence of the deduced protein is identical to a partial NH2-terminal sequence determined previously for a hybridoma/plasmacytoma growth factor and a plasmacytoma growth factor isolated from mouse T cells and macrophages, respectively. The mRNA for mouse IL-6 is expressed in IL-1-treated stromal cells and in activated T-cell and macrophage cell lines. Supernatants from COS-7 monkey cells transfected with the cDNA clone have plasmacytoma growth factor, hepatocyte-stimulating factor, and colony-stimulating factor activities, as well as the ability to support the growth of a factor-dependent myeloid cell line, thus revealing an additional biological activity for IL-6.

Amino Acid Sequence↗

PubMed1988

Structure and expression of spinach leaf cDNA encoding ribulosebisphosphate carboxylase/oxygenase activase.

Ribulosebisphosphate carboxylase/oxygenase activase is a recently discovered enzyme that catalyzes the activation of ribulose-1,5-bisphosphate carboxylase/oxygenase ["rubisco"; ribulose-bisphosphate carboxylase; 3-phospho-D-glycerate carboxy-lyase (dimerizing), EC 4.1.1.39] in vivo. Clones of rubisco activase cDNA were isolated immunologically from spinach (Spinacea oleracea L.) and Arabidopsis thaliana libraries. Sequence analysis of the spinach and Arabidopsis cDNAs identified consensus nucleotide binding sites, consistent with an ATP requirement for rubisco activase activity. A derived amino acid sequence common to chloroplast transit peptides was also identified. After synthesis of rubisco activase in vitro, the transit peptide was cleaved and the protein was transported into isolated chloroplasts. Analysis of spinach and Arabidopsis nuclear DNA by hybridization indicated a single rubisco activase gene in each species. Leaves of spinach and Arabidopsis wild type contained a single 1.9-kilobase rubisco activase mRNA. In an Arabidopsis mutant lacking rubisco activase protein, mRNA species of 1.7 and 2.1 kilobases were observed under conditions of high-stringency hybridization with a wild-type cDNA probe. This observation indicates that the lesion in the mutant arises from an error in mRNA processing.

Amino Acid Sequence↗

PubMed1989

Molecular cloning of a murine fibronectin receptor and its expression during inflammation. Expression of VLA-5 is increased in activated peritoneal macrophages in a manner discordant from major histocompatibility complex class II.

Human fibronectin receptor (VLA-5) alpha and beta chain probes were used to identify their mouse homologues in a thioglycollate-elicited peritoneal exudate cell cDNA library. Sequence analysis of both alpha and beta chain-related murine clones revealed approximately 90% homology to their human counterparts by both nucleotide and derived amino acid sequence comparisons. Detectable alpha chain transcripts were seen predominantly in total RNA of peritoneal macrophages. beta chain expression, however, was detected at higher levels in lung, heart, brain, and kidney, suggesting the presence of a large murine VLA family similar to the human family. Analysis of levels of expression comparing resting peritoneal macrophages with macrophages elicited using inflammatory stimuli indicated that alpha chain message and surface VLA-5 expression were significantly increased using thioglycollate or Listeria monocytogenes as stimuli to elicit cells. Interestingly, beta chain message was unaffected by these inflammatory stimuli, suggesting that VLA-5 expression is regulated by VLA-5 alpha chain message levels. These results indicate that macrophage VLA-5 expression can be modulated in vivo and may provide an important mechanism by which macrophages are recruited to or adhere to fibronectin in inflammatory foci.

Amino Acid Sequence↗