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In fisheries science, life-history trait information is widely used to estimate fish population recruitment, growth, and mortality. The aging and growth of Oreochromis mossambicus from the Sundays River Valley irrigation pond in the Eastern Cape province of South Africa were determined using otoliths. Mark recapture of chemically-tagged wild fish was used to confirm the periodicity of growth zone creation. A total of 150 specimens of O. mossambicus were obtained using a combination of seine and fyke nets. Female total lengths (Lt) ranged from 20 to 340 mm, while male Lt ranged from 82 to 374 mm. Growth zone deposition rates of wild O. mossambicus otoliths fluorochrome-marked with oxytetracycline hydrochloride (OTC) and recaptured after one year was consistent with the deposition of one growth increment annually. According to the three-parameter von Bertalanffy model, growth was described using different coefficients for females and males, respectively. The maximum age estimate for both females and males was 12 years. Oreochromis mossambicus in this warm temperate pond had relatively long life spans compared to subtropical populations, which suggest likely long-term population persistence within cooler, novel environments. [ABSTRACT FROM AUTHOR]

Exosomes are small extracellular vesicles secreted by various cell types, playing a crucial role in intercellular communication by carrying proteins, lipids, and nucleic acids, thus holding significant potential in diagnostics and therapeutics. Accurate labeling of exosomes is vital for studying their biogenesis, trafficking, and functional properties, enabling precise tracking and manipulation. This review examines current labeling techniques, including metabolic glycan labeling, chemical tagging, membrane fluorescent dyes, bio-conjugation, non-covalent labeling, and cell-engineering approaches. Each method is analyzed for its efficiency, specificity, and practicality, with attention to potential artifacts and challenges. Advancements in these techniques are essential for improving our understanding of exosome biology and developing exosome-based diagnostic and therapeutic strategies, providing researchers with valuable insights into state-of-the-art techniques and their applications in exosome research., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Quinones are among the most important components in natural organic matter (NOM) for redox reactions; however, no quinones in complex environmental media have been identified. To aid the identification of quinone-containing molecules in ultracomplex environmental samples, we developed a chemical tagging method that makes use of a Michael addition reaction between quinones and thiols (-SH) in cysteine (Cys) and cysteine-contained peptides (CCP). After the tagging, candidates of quinones in representative aqueous environmental samples (water extractions of biochar) were identified through high-resolution mass spectrometry (HRMS) analysis. The MS and UV spectra analysis showed rapid reactions between Cys/CCP and model quinones with β-carbon from the same benzene ring available for Michael addition. The tagging efficiency was not influenced by other co-occurring nonquinone representative compounds, including caffeic acid, cinnamic acid, and coumaric acid. Cys and CCP were used to tag quinones in water extractions of biochars, and possible candidates of quinones (20 and 53 based on tagging with Cys and CCP, respectively) were identified based on the HRMS features for products of reactions with Cys/CCP. This study has successfully demonstrated that such a Michael addition reaction can be used to tag quinones in complex environmental media and potentially determine their identities. The method will enable an in-depth understanding of the redox chemistry of NOM and its critical chemical compositions and structures.

The elucidation of distinct protein conformers or states by fluorine ((19)F) NMR requires fluorinated moieties whose chemical shifts are most sensitive to subtle changes in the local dielectric and magnetic shielding environment. In this study we evaluate the effective chemical shift dispersion of a number of thiol-reactive trifluoromethyl probes [i.e. 2-bromo-N-(4-(trifluoromethyl)phenyl)acetamide (BTFMA), N-(4-bromo-3-(trifluoromethyl)phenyl)acetamide (3-BTFMA), 3-bromo-1,1,1-trifluoropropan-2-ol (BTFP), 1-bromo-3,3,4,4,4-pentafluorobutan-2-one (BPFB), 3-bromo-1,1,1-trifluoropropan-2-one (BTFA), and 2,2,2-trifluoroethyl-1-thiol (TFET)] under conditions of varying polarity. In considering the sensitivity of the (19)F NMR chemical shift to the local environment, a series of methanol/water mixtures were prepared, ranging from relatively non-polar (MeOH:H2O = 4) to polar (MeOH:H2O = 0.25). (19)F NMR spectra of the tripeptide, glutathione ((2S)-2-amino-4-{[(1R)-1-[(carboxymethyl)carbamoyl]-2-sulfanylethyl]carbamoyl}butanoic acid), conjugated to each of the above trifluoromethyl probes, revealed that the BTFMA tag exhibited a significantly greater range of chemical shift as a function of solvent polarity than did either BTFA or TFET. DFT calculations using the B3LYP hybrid functional and the 6-31G(d,p) basis set, confirmed the observed trend in chemical shift dispersion with solvent polarity.

Noncoding RNAs (ncRNAs) comprise a class of versatile transcripts that are highly involved in the regulation of a wide range of biological processes. Functional long ncRNAs (> 200 nts in length) often adopt secondary structures that arise co-transcriptionally. To maintain the secondary structure elements as well as preparation homogeneity of such transcripts, native-like conditions should be maintained throughout the in vitro synthesis, purification and chemical tagging processes. In this optimized protocol, we describe a simple method for obtaining homogenous samples followed by chemically tagging the 3′ termini of natively-purified structured ncRNA domains that are longer than 200 nts. This protocol replaces traditional hazardous radioactive labeling with fluorescence tagging, and eliminates laborious and time consuming RNA purification and concentration steps and replaces them with straightforward recovery of RNA through centrifugal filtration, preserving the homogeneity and mono-dispersion of the preparations. The protocol provides: • An integrative, simple and straightforward approach for synthesis, purification and labeling of structured ncRNAs whilst maintaining their secondary structure intact. • Replacing hazardous, laborious and time-consuming radioactive labeling of RNA with much simpler fluorescence tagging, thereby facilitating potential downstream applications such as electrophoretic mobility shift assay (EMSA). • A versatile protocol that could be applicable to a wide-range of chemical tags and in principle could be used to label DNA or RNA.

Stocking of native fishes is conducted to augment riverine fisheries in many parts of the world, yet most stocking activities are conducted without empirical information on their effectiveness or impacts. In the Murray-Darling Basin (MDB), Australia, stocking has been underway for several decades to maintain recreational fisheries. We stocked chemically tagged golden perch (Macquaria ambigua) fingerlings in three rivers to determine the proportions of stocked fish within populations of the species. Stocked sites were monitored for up to 5 years in the Murrumbidgee River, Edward River and Billabong Creek and non-stocked sites were monitored in the Murray River. Catch per unit effort of stocked year classes increased substantially in Billabong Creek, with stocked fish contributing 100 (2005), 79 (2006) and 92% (2007). Chemically tagged fish comprised 18-38% of the respective age classes in the Murrumbidgee and Edward rivers and there was little evidence of natural recruitment in the non-stocked Murray River. Tagged fish generally attained the legal minimum size within 4 years and had dispersed up to 60 km from the original release location. Our results demonstrate that artificial stocking has the potential to strongly influence the abundance and population structure of golden perch in rivers of the MDB. [ABSTRACT FROM AUTHOR]

The elucidation of distinct protein conformers or states by fluorine (F) NMR requires fluorinated moieties whose chemical shifts are most sensitive to subtle changes in the local dielectric and magnetic shielding environment. In this study we evaluate the effective chemical shift dispersion of a number of thiol-reactive trifluoromethyl probes [i.e. 2-bromo- N-(4-(trifluoromethyl)phenyl)acetamide (BTFMA), N-(4-bromo-3-(trifluoromethyl)phenyl)acetamide (3-BTFMA), 3-bromo-1,1,1-trifluoropropan-2-ol (BTFP), 1-bromo-3,3,4,4,4-pentafluorobutan-2-one (BPFB), 3-bromo-1,1,1-trifluoropropan-2-one (BTFA), and 2,2,2-trifluoroethyl-1-thiol (TFET)] under conditions of varying polarity. In considering the sensitivity of the F NMR chemical shift to the local environment, a series of methanol/water mixtures were prepared, ranging from relatively non-polar (MeOH:HO = 4) to polar (MeOH:HO = 0.25). F NMR spectra of the tripeptide, glutathione (( 2S)-2-amino-4-{[(1 R)-1-[(carboxymethyl)carbamoyl]-2-sulfanylethyl]carbamoyl}butanoic acid), conjugated to each of the above trifluoromethyl probes, revealed that the BTFMA tag exhibited a significantly greater range of chemical shift as a function of solvent polarity than did either BTFA or TFET. DFT calculations using the B3LYP hybrid functional and the 6-31G(d,p) basis set, confirmed the observed trend in chemical shift dispersion with solvent polarity. [ABSTRACT FROM AUTHOR]

Graphene oxide (GO) is chemically tagged with polyurethane matrix and thereby prepared a polymer nanocomposite gel and compared its property development with respect to physically GO mixed polyurethane composite. Very high gelation rate is observed for GO tagged polymer along with its formation at higher temperature as compared to physical mixture. The thermal (gel melting and solvent retention power) and mechanical stabilities have significantly been improved in chemically tagged nanocomposite gel. The interaction between GO and polyurethane, responsible for improved properties, has been verified through spectroscopic measurements, from the shifting of peak position. The detail rheological measurements such as frequency sweep, steady shear, constant shear and stress relaxation analyses are performed to understand the effect of chemical tagging of GO with the polymer chains. The storage moduli (G ′) show almost parallel to x-axis with increasing frequency for the nanocomposite gels of chemically tagged species while it slightly increase, especially at higher frequency, in pure polyurethane gel. The gel strengths are found to be 88, 560 and 12844 Pa for pure PU, physical and chemical gel, respectively. The viscosity of chemically tagged nanocomposite gel is significantly higher as compared to the pure, and physically tagged polymer gels (both the steady and dynamic state). Nanocomposite gels exhibit better elastic properties as evident from quite stable relaxation moduli even at longer time as opposed to pure polymer gel where considerably sharp decrease of modulus is observed. However, the chemical tagging of GO improves the properties of the polymer gel for their wider applications. [Display omitted] • Graphene oxide is chemically tagged with polyurethane chain to produce nanocomposite. • Gelation of the graphene tagged nanocomposites have studied and compared with pure PU. • Rheological studies of chemically tagged gel have been performed for its suitability in applications. • Comparison of physical and chemical gels have been done in terms of interaction and properties. [ABSTRACT FROM AUTHOR]

Abstract: Irreversible modification is one of the most promising strategies to identify cellular receptors of bioactive small molecules. Here we report that receptor proteins can be chemically tagged using a 5-sulfonyl tetrazole probe. 5-Sulfonyl tetrazole easily accepted nucleophilic attack of thiol groups, while 5-sulfinyl tetrazole did not. These functional groups were introduced into probe molecules of a natural product. Cyclosporine A, an immunosuppressant produced by a microbe, was derivatized to possess 5-sulfonyl tetrazole and a tag group, which enabled chemical tagging of cyclophilin A, the cellular receptor of cyclosporine A. Cyclosporine A derivative possessing 5-sulfinyl tetrazole could not tag cyclophilin A. This technique will allow efficient identification of cellular receptors of bioactive small molecules. [Copyright &y& Elsevier]

We tested the hypothesis that growth zones in the astericus otoliths of smallmouth yellowfish (Labeobarbus aeneus) and Orange River mudfish (Labeo capensis) were deposited annually. Two methods, fluorochrome marking and edge analysis of otoliths were used. For fluorochrome marking, specimens of both species were injected with 60 mg/kg fish mass oxytetracycline hydrochloride (OTC) and released into large earthen ponds under ambient conditions adjacent to Lake Gariep. Twenty-three L. aeneus and one L. capensis were recaptured 10-14 months later. Edge analysis was based on the optical interpretation of L. aeneus (n = 342) and L. capensis (n = 512) otolith margins collected between November 2006 and May 2008 from Lake Gariep. The frequency distribution of opaque margins over time was fitted using a binomial periodic regression. The estimated cycle length was not significantly different from a hypothesized 12 months for both species. The number of growth zones distal to the OTC mark was consistent with findings from the edge analysis, providing evidence that growth zones in astericus otoliths of both species can be interpreted as annuli. [ABSTRACT FROM AUTHOR]

• Calcein marks were retained in fish for over 1200 days. • The Parasphenoid of fish retained marks for 630 days in outdoor raceways. • Fish that were frozen had significantly less luminous marks on their otoliths. Marking and tagging fish is an important tool used in fisheries management. Calcein has shown potential as a marking agent for fish, but it is limited in field applications by sunlight degradation. In this study, three experiments were conducted to determine the long-term retention, effect of sunlight exposure, and the effect of freezing on calcein marks in unprocessed Lake trout Salvelinus namaycush samples. In experiment one the duration of calcein mark retention in Lake trout reared indoors was measured over a 1200-day period. Calcein marks were present throughout the 1200-day study in the head-jaw and caudal fins, however marks were not observed in otoliths or scales. Experiment two shows that sunlight had an adverse effect on mark retention over a period of 630 days. Fish reared in sunlight lost their markings in most tissues by day 150, but the parasphenoid and vertebrae retained markings throughout the study. Fish reared indoors in this study retained their calcein mark, although the percentage of fish with identifiable marks declined. In experiment three, the presence of calcein marks was evident throughout the experimental period, however freezing reduced mark intensity significantly in otoliths (P < 0.05) at day 30, 90, 180, and 270 post freezing compared to non-frozen Lake trout samples. No significant differences in reduced mark intensity (P> 0.05) by freezing occurred in the head-jaw, dorsal, caudal, or anal fins, and body scales, but variation increased across all tissues. No calcein marks could be observed in otolith and scale samples stored frozen for 36–72 months in experiment 1 and 2. This study found that sunlight exposure and extended frozen storage present limitations in calcein related research, however the parasphenoid and vertebrae were less affected by these two variables. These results provide useful information on the applicability and limitations of calcein in management settings and show that the parasphenoid is an excellent location for mark detection. [ABSTRACT FROM AUTHOR]

We have applied the chemical tagging technique to study three old Open Clusters (NGC2632/Praesepe, NGC752 and NGC1817) by using our own spectral analysis code. [ABSTRACT FROM PUBLISHER]