Munoz ET et al. (2004) BMC Genomics "Microarray and EST database estimates of mRNA expression levels differ: the protein length versus expression curve for C. elegans."

Bogarad LD, Munoz ET, Deem MW

[BMC Genomics, 2004]

Background: Various methods for estimating protein expression levels are known. The level of correlation between these methods is only fair, and systematic biases in each of the methods cannot be ruled out. We here investigate systematic biases in the estimation of gene expression rates from microarray data and from abundance within the Expressed Sequence Tag (EST) database. We suggest that length is a significant factor in biases to measured gene expression rates. As a specific example of the importance of the bias of expression rate with length, we address the following evolutionary question: Does the average C. elegans protein length increase or decrease with expression level? Two different answers to this question have been reported in the literature, one method using expression levels estimated by abundance within the EST database and another using microarrays. We have investigated this issue by constructing the full protein length versus expression curve for C. elegans, using both methods for estimating expression levels. Results: The microarray data show a monotonic decrease of length with expression level, whereas the abundance within the EST database data show a non-monotonic behavior. Furthermore, the ratio of the expression level estimated by the EST database to that measured by microarrays is not constant, but rather systematically biased with gene length. Conclusions: It is suggested that the length bias may lie primarily in the abundance within the EST database method, being not ameliorated by internal standards as it is in the microarray data, and that this bias should be removed before data interpretation. When this is done, both the microarray and the abundance within the EST database give a monotonic decrease of spliced length with expression level, and the correlation between the EST and microarray data becomes larger. We suggest that standard RNA controls be used to normalize for length bias in any method that measures expression.

Pang S et al. (2010) Lab Chip "Implementation of a color-capable optofluidic microscope on a RGB CMOS color sensor chip substrate."

Wang YM, Yang C, DeModena J, Cui X, Sternberg P, Pang S

[Lab Chip, 2010]

We report the implementation of a color-capable on-chip lensless microscope system, termed color optofluidic microscope (color OFM), and demonstrate imaging of double stained Caenorhabditis elegans with lacZ gene expression at a light intensity about 10 mW/cm(2).

Rand JB et al. (1985) J Neurochem "Properties and partial purification of choline acetyltransferase from the nematode Caenorhabditis elegans."

Rand JB, Russell RL

[J Neurochem, 1985]

We have stabilized and studied choline acetyltransferase from the nematode Caenorhabditis elegans. The enzyme is soluble, and two discrete forms were resolved by gel filtration. The larger of these two forms (MW approximately 154,000) was somewhat unstable and in the presence of 0.5 M NaI was converted to a form indistinguishable from the "native" small form (MW approximately 71,000). We have purified the small form of the enzyme greater than 3,300-fold by a combination of gel filtration, ion-exchange chromatography, and nucleotide affinity chromatography. The purified preparation has a measured specific activity of 3.74 mumol/min/mg protein, and is free of acetylcholinesterase and acetyl-CoA hydrolase activities. The Vmax of the purified enzyme is stimulated by NaCl, with half-maximal stimulation at 80 mM NaCl. The Km for each substrate is also affected by salt, but in different manners from each other and the Vmax; the kinetic parameter Vmax/Km thus changes significantly as a function of the salt concentration.

Zuckerman BM et al. (1991) International C. elegans Meeting "A MICROBIAL EGG-LAYING INHIBITING FACTOR FOR CAENORHABDITIS ELEGANS."

Zuckerman BM, Willett JW, Dicklow MB

[International C. elegans Meeting, 1991]

A microbial exometabolite (ME) has been isolated which inhibits egg- laying in Caenorhabditis elegans. Nematodes exposed to active concentrations of the factor, and maintained at 22C in axenic culture ( liver extract medium), mature and grow normally. Eggs are fertilized and larvae develop and move within eggs as in untreated nematodes. However, eggs are not laid, though occasionally hatch occurs within the gonad. In shake culture of the microbe, active yellow-pigmented ME appears at 3-4 days. A concentration of 8 parts ME: 1 part liver extract completely inhibits egg-laying. Concentrations of 4 ME: 1 liver extract and 2 ME: 1 liver extract, inhibit egg-laying about 50 and 25%, respectively. Sections from nematodes exposed to extracts of a microbe showing similar properties examined by transmission electron microscopy indicated that the constrictor and dilator muscles associated with vulval function in egg-laying appear normal. ME is thermostable (at 100C for 5 min.), and the active fraction does not pass through 6,000-8,000 MW dialysis tubing. About one-half of the activity is lost when ME is dialyzed through 12,000 14,000 MW membrane tubing, suggesting the presence of at least two active fractions. Trypsinization obliterated activity. Thus far, the double control experiment with trypsin inhibitor has not yielded definitive results. SDS gel electrophoresis of boiled ME, with molecules below 8,000 MW removed by dialysis, revealed several strong protein bands, one or more of which may be ME. ME purification and characterization studies continue.

Lee JH et al. (2014) Biofouling "Thermoresponsive oligomers reduce Escherichia coli O157:H7 biofouling and virulence."

Kim YG, Kim SC, Lee J, Cho MH, Cho HS, Kim J, Lee JH

[Biofouling, 2014]

Thermoresponsive polymers have potential biomedical applications for drug delivery and tissue engineering. Here, two thermoresponsive oligomers were synthesized, viz. oligo(N-isopropylacrylamide) (ONIPAM) and oligo(N-vinylcaprolactam) (OVCL), and their anti-biofouling abilities investigated against enterohemorrhagic E. coli O157:H7, which produces Shiga-like toxins and forms biofilms. Biofilm formation (biofouling) is closely related to E. coli O157:H7 infection and constitutes a major mechanism of antimicrobial resistance. The synthetic OVCL (MW 679) and three commercial OVCLs (up to MW 54,000) at 30 g ml(-1) were found to inhibit biofouling by E. coli O157:H7 at 37 C by more than 80% without adversely affecting bacterial growth. The anti-biofouling activity of ONIPAM was weaker than that of OVCL. However, at 25 C, ONIPAM and OVCL did not affect E. coli O157:H7 biofouling. Transcriptional analysis showed that OVCL temperature-dependently downregulated curli genes in E. coli O157:H7, and this finding was in line with observed reductions in fimbriae production and biofouling. In addition, OVCL downregulated the Shiga-like toxin genes stx1 and stx2 in E. coli O157:H7 and attenuated its in vivo virulence in the nematode Caenorhabditis elegans. These results suggest that OVCL has potential use in antivirulence strategies against persistent E. coli O157:H7 infection.

de Pomerai DI et al. (2003) FEBS Lett "Microwave radiation can alter protein conformation without bulk heating."

Jones D, Duce IR, de Pomerai DI, Smith B, Dawe A, Archer DB, Smith T, North K, Candido EPM

[FEBS Lett, 2003]

Exposure to microwave radiation enhances the aggregation of bovine serum albumin in vitro in a time- and temperature-dependent manner. Microwave radiation also promotes amyloid fibril formation by bovine insulin at 60degreesC. These alterations in protein conformation are not accompanied by measurable temperature changes, consistent with estimates from field modelling of the specific absorbed radiation (15-20 mW kg(-1)). Limited denaturation of cellular proteins could explain our previous observation that modest heat-shock responses are induced by microwave exposure in Caenorhabditis elegans. We also show that heat-shock responses both to heat and microwaves are suppressed after RNA interference ablating heat-shock factor function.

Wiegner O et al. (1996) Worm Breeder's Gazette "Large communication channels in C. elegans embryos"

Bossinger O, Schierenberg E, Wiegner O

[Worm Breeder's Gazette, 1996]

The pattern of cell-cell communication in embryos of C.elegans has beeninvestigated by injecting tracer dyes into individual blastomeres (Bossinger and Schierenberg, 1992). It has been shown that in embryos from the 4-cell stage onward all blastomeres are well coupled for the diffusion of negatively charged Lucifer Yellow (LY; MW 457 Da) while uncharged Rhodamin-coupled dextran (MW 4.000 - 70.000 Da) remains restricted to the injected cell and its descendants. However, in Cephalobus spec. (another soil nematode), LY and Rhodamin-dextran (even at a molecular weight of 70.000 Da) diffuse along discrete pathways from cell to cell (Bossinger and Schierenberg, 1996). We extended our dye-coupling studies in C. elegans using negatively charged dextrans (LY-dextran and FITC-dextran) with molecular weights of 10.000 and 70.000 Da. Suprisingly, we found that in embryos between the 4-and the 24-cell stage all blastomeres are coupled for negatively charged dextrans whereas under all tested conditions uncharged Rhodamin-dextran (MW 10.000 Da) remains in the injected cell and its descendants. The diffusion of the negatively charged dyes appears to occur quickly and freely between all blastomeres. In contrast to Cephalobus we did not observe preferential pathways of dye spread from the injected cell, suggesting that all blastomeres are equally coupled. However at the 24-cell stage, when the primordial germline cell P4 has been generated, diffusion into D and P4 cells becomes retarded.The diffusion block lasts approximately 5 minutes until D joins the somatic compartment and P4 remains uncoupled for at least 20 min. A similar observation has been made for the much smaller LY in C. elegans indicating that it is a diffusion block and not a reduction in channel diameter. In summary, our findings suggest that in the developing C. elegans embryo all somatic blastomeres are coupled by communication channels much larger than conventional gap junctions. These channels seem to be permeable for negatively charged molecules up to a molecular weight of at least 70.000 Da but are impermeable to uncharged dextrans. Moreover, these channels seem to be equally present between all blastomeres of the somatic cells. Presently we can only speculate about the function of these communication pathways. Bossinger, O; Schierenberg, E. (1992) Dev. Biol. 151: 401-409 Bossinger, O; Schierenberg, E. (1996) Dev. Genes Evol. 206: 25-34

He H et al. (2022) Opt Lett "890-nm-excited SHG and fluorescence imaging enabled by an all-fiber mode-locked laser."

Ran Q, Wong KKY, Ko H, He H, Zheng C, Ren YX, Lai HM, Zhou M, Tsia KK, Qiao T

[Opt Lett, 2022]

We demonstrate second-harmonic generation (SHG) microscopy excited by the ∼890-nm light frequency-doubled from a 137-fs, 19.4-MHz, and 300-mW all-fiber mode-locked laser centered at 1780 nm. The mode-locking at the 1.7-um window is realized by controlling the emission peak of the gain fiber, and uses the dispersion management technique to broaden the optical spectrum up to 30 nm. The spectrum is maintained during the amplification and the pulse is compressed by single-mode fibers. The SHG imaging performance is showcased on a mouse skull, leg, and tail. Two-photon fluorescence imaging is also demonstrated on C. elegans labeled with green and red fluorescent proteins. The frequency-doubled all-fiber laser system provides a compact and efficient tool for SHG and fluorescence microscopy.

Francis GR et al. (1982) Worm Breeder's Gazette "minor structural proteins of C elegans muscle."

Waterston RH, Francis GR

[Worm Breeder's Gazette, 1982]

We have sought to identify minor structural proteins of C. elegans muscle with the eventual aim of characterizing genes encoding them. For this purpose, antibodies are being raised to minor bands present in extracts of broken cuticles with muscle fibrils still attached, prepared by limited French press shearing and repeated low-speed sedimentations in low ionic strength buffer containing nonionic detergent. By polarizing and electron microscopy the bodywall musculature remains associated with the cuticle through this treatment without gross structural alterations while nuclei and other cytoplasmic constituents are washed away. Of the antisera prepared so far, the most interesting is a rabbit antibody to a 107,000 MW protein which by indirect immunofluorescence stains the dense-bodies of the bodywall musculature [the dense bodies serve as thin filament anchors analogous to the z-disc of vertebrate skeletal muscle]. As this protein cross-reacts with an antibody to smooth muscle alpha-actinin ( a component of smooth muscle dense-bodies) on nitrocellulose replicas of SDS-gels we presume it to be an alpha-actinin-like protein and are doing further experiments to test homology. Antibodies to other purified polypeptides appear to recognize intermediate filaments or hypodermal cell structures limited to areas beneath the bodywall musculature that may be responsible for transmitting muscle tension to the cuticle. Finally, an antibody to a 230,000 MW polypeptide lights up the nervous system circuitry: nerve ring, head neurons, dorsal and ventral cords, commisures, etc. Although this antigen is uncharacterized, it could be the macromolecule recognized by peanut agglutinin which, by lectin fluorescence, is present in the broken and washed cuticles. Currently mutants are being screened with these antibodies by immunofluorescence and two-dimensional electrophoresis but as yet we have no gene-protein correlations.

Zacchino SA et al. (2017) Phytomedicine "Hybrid combinations containing natural products and antimicrobial drugs that interfere with bacterial and fungal biofilms."

Zacchino SA, Butassi E, Svetaz LA, Cordisco E

[Phytomedicine, 2017]

BACKGROUND: Biofilms contribute to the pathogenesis of many chronic and difficult-to eradicate infections whose treatment is complicated due to the intrinsic resistance to conventional antibiotics. As a consequence, there is an urgent need for strategies that can be used for the prevention and treatment of biofilm-associated infections. The combination therapy comprising an antimicrobial drug with a low molecular weight (MW) natural product and an antimicrobial drug (antifungal or antibacterial) appeared as a good alternative to eradicate biofilms. PURPOSE: The aims of this review were to perform a literature search on the different natural products that have showed the ability of potentiating the antibiofilm capacity of antimicrobial drugs, to analyze which are the antimicrobial drugs most used in combination, and to have a look on the microbial species most used to prepare biofilms. RESULTS: Seventeen papers, nine on combinations against antifungal biofilms and eight against antibacterial biofilms were collected. Within the text, the following topics have been developed: breaf history of the discovery of biofilms; stages in the development of a biofilm; the most used methodologies to assess antibiofilm-activity; the natural products with capacity of eradicating biofilms when acting alone; the combinations of low MW natural products with antibiotics or antifungal drugs as a strategy for eradicating microbial biofilms and a list of the low MW natural products that potentiate the inhibition capacity of antifungal and antibacterial drugs against biofilms. CONCLUSIONS AND PERSPECTIVES: Regarding combinations against antifungal biofilms, eight over the nine collected works were carried out with in vitro studies while only one was performed with in vivo assays by using Caenorhabditis elegans nematode. All studies use biofilms of the Candida genus. A 67% of the potentiators were monoterpenes and sesquiterpenes and six over the nine works used FCZ as the antifungal drug. The activity of AmpB and Caspo was enhanced in one and two works respectively. Regarding combinations against bacterial biofilms, in vitro studies were performed in all works by using several different methods of higher variety than the used against fungal biofilms. Biofilms of both the gram (+) and gram (-) bacteria were prepared, although biofilm of Staphylococcus spp. were the most used in the collected works. Among the discovered potentiators of antibacterial drugs, 75% were terpenes, including mono, di- and triterpenes, and, among the atibacterial drugs, several structurally diverse types were used in the combinations: aminoglycosides, -lactams, glucopeptides and fluoroquinolones. The potentiating capacity of natural products, mainly terpenes, on the antibiofilm effect of antimicrobial drugs opens a wide range of possibilities for the combination antimicrobial therapy. More in vivo studies on combinations of natural products with antimicrobial drugs acting against biofilms are highly required to cope the difficult to treat biofilm-associated infections.