gebhart/patrepeval huggingface dataset:
Formation of the embryonic-abembryonic axis of the mouse blastocyst:relationships between orientation of early cleavage divisions and pattern of symmetric/asymmetric divisions (2008)

Setting aside pluripotent cells that give rise to the future body is a central cell fate decision in mammalian development. It requires that some blastomeres divide asymmetrically to direct cells to the inside of the embryo. Despite its importance, it is unknown whether the decision to divide symmetrically versus asymmetrically shows any spatial or temporal pattern, whether it is lineage-dependent or occurs at random, or whether it influences the orientation of the embryonic-abembryonic axis. To address these questions, we developed time-lapse microscopy to enable a complete 3D analysis of the origins, fates and divisions of all cells from the 2- to 32-cell blastocyst stage. This showed how in the majority of embryos, individual blastomeres give rise to distinct blastocyst regions. Tracking the division orientation of all cells revealed a spatial and temporal relationship between symmetric and asymmetric divisions and how this contributes to the generation of inside and outside cells and thus embryo patterning. We found that the blastocyst cavity, defining the abembryonic pole, forms where symmetric divisions predominate. Tracking cell ancestry indicated that the pattern of symmetric/asymmetric divisions of a blastomere can be influenced by its origin in relation to the animal-vegetal axis of the zygote. Thus, it appears that the orientation of the embryonic-abembryonic axis is anticipated by earlier cell division patterns. Together, our results suggest that two steps influence the allocation of cells to the blastocyst. The first step, involving orientation of 2- to 4-cell divisions along the animal-vegetal axis, can affect the second step, the establishment of inside and outside cell populations by asymmetric 8- to 32-cell divisions.
Applications of hydrogels for neural cell engineering (2007)

Hydrogels, three-dimensional networks of hydrophilic polymers, are currently being investigated for use in a variety of tissue-engineering applications. Hydrogel materials generally exhibit a number of properties including permeability to oxygen and nutrients, which make these materials attractive for use in biological applications. However, in order for such polymers to be successfully integrated into biological systems, these constructs must be engineered so as to mimic native biological interfaces. In this paper we discuss the use of acrylate-based polymers and their derivatives, for use in biomedical applications, including drug delivery, tissue engineering, cell encapsulation, and as templates for directed cell growth, attachment and proliferation.
Cytokine secretion by CD4 T lymphocytes acquired in response to Mycobacterium tuberculosis infection. (1993)

The results of this study, in which CD4 T cells were harvested from mice at various times during the course of a virulent Mycobacterium tuberculosis infection and examined for their secretion of cytokines during culture in vitro with bone marrow-derived macrophages presenting mycobacterial Ag, provide evidence for the existence of two separate waves of cytokine-producing CD4 cells. The first, which peaks at the time at which protective immunity was maximally expressed, was characterized as a IFN-gamma-secreting cell population that preferentially recognized macrophages presenting mycobacterial culture filtrate proteins, or that were infected with the live organism. A second population, which emerged 20 to 40 days later at a time when the infection had been contained, secreted IL-4 in response to the filtrate proteins, but also reacted particularly strongly to the 65-kDa (hsp60) heat shock protein molecule of M. tuberculosis. These data indicate that acquired immunity to tuberculosis infection involves the production of both Th1- and Th2-like cell populations that differ in terms of their kinetics of emergence and loss, and in terms of their Ag specificity.
Permanently microbicidal materials coatings (2007)

Recently developed non-leaching, permanently microbicidal polymeric coatings are discussed. These coatings, comprising hydrophobic polycations either covalently attached or deposited (“painted”) onto surfaces of diverse materials, avidly kill human pathogenic bacteria, fungi, and viruses (but not mammalian cells) on contact by disrupting their lipid membranes.
Minimization of exogenous signals in ES cell culture induces rostral hypothalamic differentiation (2008)

Embryonic stem (ES) cells differentiate into neuroectodermal progenitors when cultured as floating aggregates in serum-free conditions. Here, we show that strict removal of exogenous patterning factors during early differentiation steps induces efficient generation of rostral hypothalamic-like progenitors (Rax(+)/Six3(+)/Vax1(+)) in mouse ES cell-derived neuroectodermal cells. The use of growth factor-free chemically defined medium is critical and even the presence of exogenous insulin, which is commonly used in cell culture, strongly inhibits the differentiation via the Akt-dependent pathway. The ES cell-derived Rax(+) progenitors generate Otp(+)/Brn2(+) neuronal precursors (characteristic of rostral-dorsal hypothalamic neurons) and subsequently magnocellular vasopressinergic neurons that efficiently release the hormone upon stimulation. Differentiation markers of rostral-ventral hypothalamic precursors and neurons are induced from ES cell-derived Rax(+) progenitors by treatment with Shh. Thus, in the absence of exogenous growth factors in medium, the ES cell-derived neuroectodermal cells spontaneously differentiate into rostral (particularly rostral-dorsal) hypothalamic-like progenitors, which generate characteristic hypothalamic neuroendocrine neurons in a stepwise fashion, as observed in vivo. These findings indicate that, instead of the addition of inductive signals, minimization of exogenous patterning signaling plays a key role in rostral hypothalamic specification of neural progenitors derived from pluripotent cells.
Magnetic tweezers for DNA micromanipulation (2000)

We detail the design of an electromagnetic assembly capable of generating a constant magnetic field superimposed to a large magnetic field gradient (between 40 and 100 T/m), which was uniform over a large gap (between 1.5 and 2 cm). Large gaps allowed the use of wide high numerical-aperture lenses to track microspheres attached to DNA molecules with an inverted light microscope. Given the geometric constraints of the microscope, computer-aided design was used to optimize the magnetic field gradient linearity, homogeneity, and amplitude, as well as the arrangement of the magnetic coils, the currents, and the mechanical stability of the assembly. The assembly was used to apply forces of controlled amplitude, direction, and time dependence on superparamagnetic microspheres by using magnetic coils instead of permanent magnets. A streptavidin-coated microsphere was attached to the 3′ end of a λ-phage DNA molecule through a single biotin molecule. The 5′ end of the λ-phage DNA molecule was tethered to a glass coverslip by conjugating the DNA’s overhang to a complementary 12 base-pair primer, which was itself cross-linked to a heterobifunctional group placed on the glass coverslip. By tracking the centroid of this microsphere, the mechanical response of a single λ-phage DNA molecule was measured as a function of the applied magnetic force. The resulting force-extension curve was fitted with the worm-like-chain model to obtain λ-phage DNA’s persistence length and contour length, which were in agreement with previous reports.
Purification and Characterization of a Lipase fromAspergillus oryzae (1995)

A lipase from Aspergillus oryzae was purified by ammonium sulfate fractionation, anion exchange chromatography, hydrophobic interaction chromatography, and anion exchange chromatography. The purified enzyme was a monomeric protein with a molecular mass of 41 kDa estimated by SDS-PAGE and 39 kDa by gel filtration. The optimum pH at 30 degrees C and optimum temperature at pH 7.0 were 7.0 and 30 degrees C, respectively. The enzyme was stable over a pH range of 6-9 at 25 degrees C for 18 h, and up to 30 degrees C at pH 7.0 for 3 h. Ag+, Fe3+, Hg2+, Cu2+, and Zn2+ inhibited the enzyme activity severely. The enzyme was a lipase that hydrolyzed monoacylglycerols and diacylglycerols, but did not hydrolyze triacylglycerols. The N-terminal amino acid sequence of the enzyme was highly homologous with that of the mono- and diacylglycerol lipase from Penicillium camembertii U-150.
Allopolyploidization and evolution of species with reduced floral structures in Lepidium L. (Brassicaceae) (2002)

Understanding the pattern of speciation in a group of plants is critical for understanding its morphological evolution. Lepidium is the genus with the largest variation in floral structure in Brassicaceae, a family in which the floral ground plan is remarkably stable. However, flowers in more than half of Lepidium species have reduced stamen numbers, and most of these also have reduced petals. The species with reduced flowers are geographically biased, distributed mostly in the Americas and Australia New Zealand. Previous phylogenetic studies using noncoding regions of chloroplast DNA and rDNA internal transcribed spacer were incongruent in most New World species relationships. These data, combined with the presence of many polyploid Lepidium species, implied a reticulate history of the genus but did not provide enough information to infer the evolutionary pattern of flower structures. To address this question more thoroughly, sequences of the first intron of a single copy nuclear gene, PISTILLATA, were determined from 43 species. Phylogenetic analysis of the PI intron suggests that many species in the New World have originated from allopolyploidization, and that this is correlated with floral reduction. Interspecific hybrids were generated to understand why allopolyploidization is associated with reduced flowers. The phenotypes of F1 flowers indicate allelic dominance of the absence of lateral stamens, suggesting that propagation of dominant alleles through interspecific hybridization could account for the abundance of the allopolyploid species without lateral stamens.
Detection of CK19, CK20 and EGFR mRNAs in peripheral blood of carcinoma patients: correlation with clinical stage of disease (2003)

Expression of genes such as cytokeratin 19 (CK19), cytokeratin 20 (CK20) and epidermal growth factor receptor (EGFR) has been investigated at mRNA level in peripheral blood of carcinoma patients to detect the presence of circulating tumor cells (CTC). We performed this study because recent literature emphasizes that the importance of CK19, 20 and EGFR mRNAs in CTC as prognostic factors remains unclear especially for breast, head and neck and colon cancer patients. Reverse transcriptase polymerase chain reaction (RT-PCR) followed by Southern blot hybridization was performed in blood samples from 47 subjects (12 colorectal, 15 head and neck and 20 breast carcinoma patients), as well as in 35 healthy donors. The CK19 expression was found in 36/47 patients (9 colorectal, 9 head and neck and 18 breast cancer), two patients (one affected by colorectal and one by head and neck cancer) were positive for CK20 whereas EGFR was found expressed in 9 patients (3 colorectal, 5 head and neck and one breast cancer). Seven of 35 and 4/35 healthy donors displayed positivity for the expression of CK19 and CK20 genes respectively, whereas no EGFR mRNA was found in this group. The correlation of the detection of CTC in peripheral blood with progression of the disease in a follow-up period of 40 months did not show any prognostic value to the presence of mRNAs of these biomarkers in blood. We believe that research should be addressed, at least for breast cancer, to the identification of occult metastases in sentinel lymph nodes, such as recently performed in melanoma patients.
The Development of Water Mist Fire Protection Systems for U.S. Navy Ships (2000)

ABSTRACT During the past 20 years, the U.S. Navy has undertaken an extensive evaluation of water mist for fire protection applications aboard ship. Both small and full‐scale tests have been conducted to study water mist as a replacement for Halon 1301 and to explore the possible use of mist in lieu of conventional sprinklers. Tests have been conducted at the David Taylor Ship Research and Development Center in Annapolis, Maryland, at the Naval Research Laboratory, Chesapeake Division, and aboard the Navy'S fire research vessel, the Ex‐Shadwell in Mobile, Alabama. Engineering analysis and trade‐off studies have been conducted to compare ship impact (cost, space and weight) of water mist versus Halon and other gaseous alternatives. As a result of the testing and analysis completed thus far, the Navy has specified water mist to protect the propulsion machinery spaces on the Navy'S next new ship, the USS San Antonio (LPD‐17), currently undergoing final design at Avondale Industries.
Basal Defenses Induced in Pepper by Lipopolysaccharides Are Suppressed by Xanthomonas campestris pv. vesicatoria (2004)

The nonpathogenic hrcC mutant of Xanthomonas campestris pv. vesicatoria 85-10::hrpA22 multiplied in pepper leaves if it was mixed with pathogenic strains of X. campestris pv. vesicatoria. Reactions to the mutant alone included localized deposition of phenolics and callose in papillae, and alterations to the plant cell wall leading to increased electron density. Electron microscopy showed that the localized responses were suppressed in the presence of wild-type bacteria but other wall changes occurred at some sites, involving cellulose-rich ingrowth of the wall. Multiplication of the hrp mutant in mixed inocula was confirmed by tagging 85-10::hrpA22 using immunocytochemical location of AvrBs3 expressed from the plasmid pD36. Elicitors of callose deposition and other wall changes were isolated from the hrcC mutant. Activity in extracts of bacteria was attributed to the presence of high molecular weight lipopolysaccharides (LPS). Wild-type X. campestris pv. vesicatoria suppressed induction of structural changes caused by purified LPS. Results obtained suggest that effector proteins produced by phytopathogenic bacteria and delivered by the type III secretion system may have a key role in suppressing the basal defense responses activated by bacterial LPS, which lead to restricted multiplication of nonpathogens such as hrp mutants.
Expanding functionality of RNA: synthesis and properties of RNA containing imidazole modified tandem G–U wobble base pairs (2005)

Imidazole modification at C-5 of uridine that is part of tandem G-U wobble base pairs causes slight reduction of thermal stability (DeltaDeltaG(0)(310) < 0.4 kcal mol(-1)) and relatively small change in hydration of short RNA helices.
Directed Evolution of Toluene ortho -Monooxygenase for Enhanced 1-Naphthol Synthesis and Chlorinated Ethene Degradation (2002)

Trichloroethylene (TCE) is the most frequently detected groundwater contaminant, and 1-naphthol is an important chemical manufacturing intermediate. Directed evolution was used to increase the activity of toluene ortho-monooxygenase (TOM) of Burkholderia cepacia G4 for both chlorinated ethenes and naphthalene oxidation. When expressed in Escherichia coli, the variant TOM-Green degraded TCE (2.5 +/- 0.3 versus 1.39 +/- 0.05 nmol/min/mg of protein), 1,1-dichloroethylene, and trans-dichloroethylene more rapidly. Whole cells expressing TOM-Green synthesized 1-naphthol at a rate that was six times faster than that mediated by the wild-type enzyme at a concentration of 0.1 mM (0.19 +/- 0.03 versus 0.029 +/- 0.004 nmol/min/mg of protein), whereas at 5 mM, the mutant enzyme was active (0.07 +/- 0.03 nmol/min/mg of protein) in contrast to the wild-type enzyme, which had no detectable activity. The regiospecificity of TOM-Green was unchanged, with greater than 97% 1-naphthol formed. The beneficial mutation of TOM-Green is the substitution of valine to alanine in position 106 of the alpha-subunit of the hydroxylase, which appears to act as a smaller "gate" to the diiron active center. This hypothesis was supported by the ability of E. coli expressing TOM-Green to oxidize the three-ring compounds, phenanthrene, fluorene, and anthracene faster than the wild-type enzyme. These results show clearly that random, in vitro protein engineering can be used to improve a large multisubunit protein for multiple functions, including environmental restoration and green chemistry.
An interferon gamma-regulated protein that binds the interferon-inducible enhancer element of major histocompatibility complex class I genes. (1990)

Interferons (IFNs) induce transcription of major histocompatibility complex (MHC) class I genes through the conserved IFN consensus sequence (ICS) that contains an IFN response motif shared by many IFN-regulated genes. By screening mouse lambda ZAP expression libraries with the ICS as a probe, we isolated a cDNA clone encoding a protein that binds the ICS, designated ICSBP. Protein blot analysis with labeled oligonucleotide probes showed that ICSBP binds not only the MHC class I ICS but also IFN response motifs of many IFN-regulated genes, as well as a virus-inducible element of the IFN-beta gene. The ICSBP cDNA encodes 424 amino acids and a long 3' untranslated sequence. The N-terminal 115 amino acids correspond to a putative DNA-binding domain and show significant sequence similarity with other cloned IFN response factors (IRF-1 and IRF-2). Because of the structural similarity and shared binding specificity, we conclude that ICSBP is a third member of the IRF gene family, presumably playing a role in IFN- and virus-mediated regulation of many genes. Although IRF-1 and IRF-2 share some similarity in their C-terminal regions, ICSBP shows no similarity to IRF-1 or IRF-2 in this region, suggesting that it is more distantly related. We show that ICSBP mRNA is expressed predominantly in lymphoid tissues and is inducible preferentially by IFN-gamma. The induction by IFN-gamma appears to be predominant in lymphocytes and macrophages, implying that ICSBP plays a regulatory role in cells of the immune system. The presence of multiple factors that bind common IFN response motifs may partly account for the complexity and diversity of IFN action as well as IFN-regulated gene expression.
In Situ “Clickable” Zwitterionic Starch-Based Hydrogel for 3D Cell Encapsulation (2016)

Three-dimensional (3D) cell encapsulation in hydrogel provides superb methods to investigate the biochemical cues in directing cellular fate and behaviors outside the organism, the primary step of which is to establish suitable "blank platform" to mimic and simplify native ECM microenvironment. In this study, zwitterionic starch-based "clickable" hydrogels were fabricated via a "copper- and light- free" Michael-type "thiol-ene" addition reaction between acylated-modified sulfobetaine-derived starch (SB-ST-A) and dithiol-functionalized poly(ethylene glycol) (PEG-SH). By incorporating antifouling SB-ST and PEG, the hydrogel system would be excellently protected from nontarget protein adsorption to act as a "blank platform". The hydrogels could rapidly gel under physiological conditions in less than 7 min. Dynamic rheology experiments suggested the stiffness of the hydrogel was close to the native tissues, and the mechanical properties as well as the gelation times and swelling behaviors could be easily tuned by varying the precursor proportions. The protein and cell adhesion assays demonstrated that the hydrogel surface could effectively resist nonspecific protein and cell adhesion. The degradation study in vitro confirmed that the hydrogel was biodegradable. A549 cells encapsulated in the hydrogel maintained high viability (up to 93%) and started to proliferate in number and extend in morphology after 2 days' culture. These results indicated the hydrogel presented here could be a potential candidate as "blank platform" for 3D cell encapsulation and biochemical cues induced cellular behavior investigation in vitro.
Separate Recombinant Antibacterial Peptide With Immobilized Metal chelated Affinity Chromatography Membranes (2000)

Immobilized metal chelated affinity chromatography (IMAC) membranes were prepared for separating a recombinant fusion antibacterial peptide ,which carried a polyhistidine sequence (HIS 6 tag) at the N terminus. Low bleeding of metal ion was achieved. It was proved that the properties of IMAC membranes were better than conventional chelating sepharose fast flow column. The fractionation of recombinant proteins that carry a polyhistidine tag is currently perhaps the most promising application of IMAC.
Evaluation of cryogen spray cooling exposure on in vitro model human skin (2004)

Continuous CSC spurts of 80 milliseconds or less induce minimal, if any, epidermal or dermal damage and are unlikely to produce cryo-injury when used during dermatologic laser surgery.
Thymidine kinase synthesis is repressed in nonreplicating muscle cells by a translational mechanism that does not affect the polysomal distribution of thymidine kinase mRNA. (1989)

The molecular basis for replication-dependent expression of thymidine kinase (TK) activity (EC 2.7.1.21) was investigated in mouse skeletal muscle cells transformed with multiple copies of the chicken TK gene. When shifted to mitogen-depleted medium, proliferating myoblasts irreversibly withdraw from the cell cycle and commit to terminal differentiation. Early after commitment, postreplicative myocytes maintain nearly proliferative levels of TK mRNA but have greatly reduced levels of TK activity. Metabolic labeling studies with [35S]methionine indicated that the decrease in TK activity was associated with a 10-fold reduction in the rate of TK protein synthesis. Commitment had little effect on the stability or catalytic efficiency of TK protein. The decrease in TK synthetic rate in the continued presence of TK mRNA indicated that translation of TK mRNA was repressed in committed cells. The distribution of TK mRNA between ribonucleoprotein particles and polysomes was determined. In both proliferative cells and committed cells, TK mRNA levels were maximal in polysomes containing five to seven ribosomes. Thus, the synthesis of TK protein in nonreplicating muscle cells was inhibited by a translational mechanism that did not alter the average number of ribosomes engaged by TK mRNA.
Detailed Mechanistic Insights into HIV-1 Sensitivity to Three Generations of Fusion Inhibitors (2009)

Peptides based on the second heptad repeat (HR2) of viral class I fusion proteins are effective inhibitors of virus entry. One such fusion inhibitor has been approved for treatment of human immunodeficiency virus-1 (T20, enfuvirtide). Resistance to T20 usually maps to the peptide binding site in HR1. To better understand fusion inhibitor potency and resistance, we combined virological, computational, and biophysical experiments with comprehensive mutational analyses and tested resistance to T20 and second and third generation inhibitors (T1249 and T2635). We found that most amino acid substitutions caused resistance to the first generation peptide T20. Only charged amino acids caused resistance to T1249, and none caused resistance to T2635. Depending on the drug, we can distinguish four mechanisms of drug resistance: reduced contact, steric obstruction, electrostatic repulsion, and electrostatic attraction. Implications for the design of novel antiviral peptide inhibitors are discussed.