Foliar phosphorus allocation and photosynthesis reveal plants' adaptative strategies to phosphorus limitation in tropical forests at different successional stages.

High atmospheric nitrogen (N) deposition and low soil phosphorus (P) availability occur simultaneously in tropical areas, and thus tropical plants need to adapt nutrient-use strategies to maintain growth and survival. Therefore, identifying the adaptative strategies of tropical plants at different successional stages under low soil P availability is indispensable. Here, we separately investigated foliar traits, photosynthetic characteristics, and P fractions of 8 species in the primary and secondary tropical forests after 10 years of N and P fertilization. P addition increased foliar P concentrations and deceased N:P ratio in the primary forest and secondary forest. The foliar photosynthetic rates did not significantly respond to nutrient additions, and the foliar photosynthetic P-use efficiency (PPUE) reduced under the P addition in the primary forest. In contrast, the foliar photosynthetic rates and photosynthetic nitrogen (N)-use efficiency (PNUE) were enhanced with nutrient additions in the secondary forest. The allocations of foliar nucleic acid P and residual P were reduced by P addition in the primary forest, whereas the allocation of metabolic P was enhanced and the allocation of residual P was reduced by P addition in the secondary forest. Additionally, a higher proportion of structural P was found in the primary forest, and a higher proportion of metabolic P was observed in the secondary forest. Interesting, structural equation model analysis revealed that the plants decreased the allocation of foliar nucleic acid P and increased the allocation of structural P in the primary forest, thereby reducing photosynthetic rates. Whereas the plants enhanced photosynthetic rates by promoting PPUE and the allocation of foliar metabolic P in the secondary forest. Our findings highlighted tropical plants at different successional stages can reasonably allocate foliar P to regulate photosynthetic rates and acclimate to low P environments.

Effects of dietary supplementation of different levels of vitamin B12 on the liver metabolism of laying hens.

BACKGROUND: Vitamin B12 plays an important role in lipid, protein, carbohydrate and nucleic acid metabolism. We investigated the effect of supplementing layers' diets with different vitamin B12 levels on liver metabolism using a liquid chromatography-mass spectrometry-based metabolomic approach to observe and analyse wide-target metabolomics in the liver. RESULTS: We assigned hens to three groups, namely blank control group without vitamin B12 diet (BCG), normal control group with 25 µg kg-1 vitamin B12 (NCG) and vitamin B12 supplement group I with 100 µg kg-1 vitamin (VBSG I). The VBSG I group layers had higher (P < 0.05) vitamin B12 concentration than those from other groups. The egg yolk vitamin B12 concentration increased (P < 0.01) with the increasing vitamin B12 dietary supplemental level. Between the NCG versus BCG, VBSG I versus BCG, and VBSG I versus NCG groups, 11, 20 and 11 metabolites were significantly changed, respectively. The KEGG pathway of vitamin B6 metabolism was significantly impacted in the NCG layers than those from BCG; seven and five pathways were significantly impacted in the VBSG I layers compared with those from BCG and NCG, including pyrimidine metabolism, vitamin B6 metabolism, glycerophospholipid metabolism, etc. CONCLUSION: We concluded that 25 µg kg-1 vitamin B12 supplementation in corn-soybean meal-based layer diet increased the egg yolk vitamin B12 concentration and impacted the vitamin B6 metabolic pathway, and 100 µg kg-1 of it increased the egg yolk and liver vitamin B12 concentrations and impacted vitamin B6 , lipid, nucleic acid and amino acid metabolic pathways. © 2022 Society of Chemical Industry.

Role of nucleic acid amplification assays in monitoring treatment response in chagas disease: Usefulness in clinical trials.

Chagas disease has become a global health problem due to migration of infected people out of Latin America to non-endemic countries. For more than 40 years, only the nitroimidazole compounds Benznidazole and Nifurtimox, have been used for specific treatment of Trypanosoma cruzi infection with disappointing results, specially due to the long duration of treatment and adverse events in the chronic phase. In the last years, ergosterol inhibitors have been also proposed for specific treatment. Different randomized clinical trials were performed for evaluating their treatment efficacy and safety. One of the greatest concerns in clinical trials is to provide an early surrogate biomarker of response to trypanocidal chemotherapy. Serological response is slow and the classical parasitological tests have poor sensitivity and are time-consuming. Nowadays, PCR is the most helpful tool for assessing treatment response in a short period of time. Different protocols of PCR have been developed, being quantitative real time PCR based on amplification of repetitive satellite or minicircle DNA sequences plus an internal amplification standard, the mostly employed strategies in clinical trials. Standardized protocols and the use of an external quality assessment ensure adequate technical procedures and reliable data. Clinical trials have shown a significant reduction in parasite loads, reaching undetectable DNA levels in bloodstream after specific treatment, however events of treatment failure have also been reported. Treatment failure could be due to inadequate penetrance of the drugs into the affected tissues, to the presence of primary or secondary drug resistance of the infecting strains as well as to the existence of dormant parasite variants reluctant to drug action. The early diagnosis of drug resistance would improve clinical management of Chagas disease patients, allowing dictating alternative therapies with a combination of existing drugs or new anti-T. cruzi agents. The aim of this review was to describe the usefulness of detecting T.cruzi DNA by means of real time PCR assays, as surrogate biomarker in clinical trials for evaluating new drugs for CD or new regimens of available drugs and the possibility to detect treatment failure.

Biochemical detection of fatal hypothermia and hyperthermia in affected rat hypothalamus tissues by Fourier transform infrared spectroscopy.

It is difficult to determinate the cause of death from exposure to fatal hypothermia and hyperthermia in forensic casework. Here, we present a state-of-the-art study that employs Fourier-transform infrared (FTIR) spectroscopy to investigate the hypothalamus tissues of fatal hypothermic, fatal hyperthermic and normothermic rats to determine forensically significant biomarkers related to fatal hypothermia and hyperthermia. Our results revealed that the spectral variations in the lipid, protein, carbohydrate and nucleic acid components are highly different for hypothalamuses after exposure to fatal hypothermic, fatal hyperthermic and normothermic conditions. In comparison with the normothermia group, the fatal hypothermia and hyperthermia groups contained higher total lipid amounts but were lower in unsaturated lipids. Additionally, their cell membranes were found to have less motional freedom. Among these three groups, the fatal hyperthermia group contained the lowest total proteins and carbohydrates and the highest aggregated and dysfunctional proteins, while the fatal hypothermia group contained the highest level of nucleic acids. In conclusion, this study demonstrates that FTIR spectroscopy has the potential to become a reliable method for the biochemical characterization of fatal hypothermia and hyperthermia hypothalamus tissues, and this could be used as a postmortem diagnostic feature in fatal hypothermia and hyperthermia deaths.

A method for analyzing the composition of viral nucleoprotein complexes, produced by heterologous expression in bacteria.

Viral genomes are protected and organized by virally encoded packaging proteins. Heterologous production of these proteins often results in formation of particles resembling the authentic viral capsid or nucleocapsid, with cellular nucleic acids packaged in place of the viral genome. Quantifying the total protein and nucleic acid content of particle preparations is a recurrent biochemical problem. We describe a method for resolving this problem, developed when characterizing particles resembling the Menangle Virus nucleocapsid. The protein content was quantified using the biuret assay, which is largely independent of amino acid composition. Bound nucleic acids were quantified by determining the phosphorus content, using inductively coupled plasma mass spectrometry. Estimates for the amount of RNA packaged within the particles were consistent with the structurally-characterized packaging mechanism. For a bacterially-produced nucleoprotein complex, phosphorus usually provides a unique elemental marker of bound nucleic acids, hence this method of analysis should be routinely applicable.

Dietary supplementation with an amino acid blend enhances intestinal function in piglets.

The traditionally classified nutritionally non-essential amino acids are now known to be insufficiently synthesized for maximal growth and optimal health in piglets. This study determined the effects of dietary supplementation with an amino acid blend (AAB; glutamate:glutamine:glycine:arginine:N-acetylcysteine = 5:2:2:1:0.5) on piglet growth performance and intestinal functions. Sixteen piglets (24-day-old) were randomly assigned to a corn and soybean meal-based diet supplemented with 0.99% alanine (isonitrogenous control) or 1% AAB. On day 20 of the trial, blood and intestinal tissue samples were obtained from piglets. Compared with the control, AAB supplementation reduced (P < 0.05) diarrhoea incidence; plasma alanine aminotransferase and diamine oxidase activities; intestinal concentrations of hydrogen peroxide, malondialdehyde, and heat shock protein-70, and intestinal mRNA levels for interleukin-1ß, interferon-γ, and chemokine (C-X-C motif) ligand-9; and the numbers of Enterobacterium family, Enterococcus genus and Clostridium coccoides in the colon digesta. Furthermore, AAB supplementation enhanced (P < 0.05): the plasma concentrations of serine, aspartate, glutamate, cysteine, tyrosine, phenylalanine, tryptophan, lysine, arginine, citrulline, ornithine, taurine, and γ-aminobutyric acid; intestinal villus height and surface area, villus height/crypt depth ratio, antioxidative enzyme activities, and mRNA levels for porcine ß-defensin-1, sodium-independent amino acid transporters (b0,+AT and y+LAT1), aquaporin (AQP) 3, AQP8, AQP10, nuclear factor erythroid 2-related factor 2 and glutathione S-transferase omega-2, and protein abundances of AQP3, AQP4, claudin-1, occludin and myxovirus resistance 1; and the numbers of Bifidobacterium genus and Lactobacillus genus in the colon digesta. Collectively, these comprehensive results indicate that dietary AAB supplementation plays an important role in improving piglet growth and intestinal function.

Application of liquid chromatography/electrospray ionization ion trap tandem mass spectrometry for the evaluation of global nucleic acids: methylation in garden cress under exposure to CuO nanoparticles.

RATIONALE: A full understanding of the biological impact of nanomaterials demands analytical procedures suitable for the detection/quantification of epigenetic changes that occur in the exposed organisms. Here, the effect of CuO nanoparticles (NPs) on global methylation of nucleic acids in Lepidium sativum was evaluated by liquid chromatography/ion trap mass spectrometry. Enhanced selectivity toward cytosine-containing nucleosides was achieved by using their proton-bound dimers formed in positive electrospray ionization (ESI(+)) as precursor ions for multiple reaction monitoring (MRM) quantification based on one or two ion transitions. METHODS: Plants were exposed to CuO NPs (0-1000 mg L(-1)); nucleic acid extracts were washed with bathocuproine disulfate; nucleosides were separated on a Luna C18 column coupled via ESI(+) to an AmaZon SL mass spectrometer (Bruker Daltonics). Cytidine, 2´-deoxycytidine, 5-methylcytidine, 5-methyl-2´-deoxycytidine and 5-hydroxymethyl-2´-deoxycytidine were quantified by MRM based on MS(3) ([2M+H](+)/[M+H](+)/[M+H-132](+) or [M+H-116](+)) and MS(2) ([2M+H](+)/[M+H](+) ). RESULTS: Bathocuproine disulfate, added as Cu(I) complexing agent, allowed for elimination of [2M+Cu](+) adducts from the mass spectra. Poorer instrumental detection limits were obtained for MS(3) (20-120 fmol) as compared to MS(2) (9.0-41 fmol); however, two ion transitions helped to eliminate matrix effects in plant extracts. The procedure was tested by analyzing salmon sperm DNA (Sigma) and applied for the evaluation of DNA and RNA methylation in plants; in the absence of NPs, 13.03% and 0.92% methylated cytosines were found in DNA and RNA, respectively; for NPs concentration >50 mg L(-1), DNA hypomethylation was observed with respect to unexposed plants. RNA methylation did not present significant changes upon plant exposure; 5-hydroxymethyl-2´-deoxycytidine was not detected in any sample. CONCLUSIONS: The MRM quantification proposed here of cytosine-containing nucleosides using their proton-bound homo-dimers as precursor ions proved its utility for the assessment of global methylation of DNA and RNA in plants under stress imposed by CuO NPs. Detection of copper adducts with cytosine-containing ions, and their elimination by washing extracts with Cu(I) chelator, calls for further investigation.

A novel adenosine-based molecular beacon probe for room temperature nucleic acid rapid detection in cotton thread device.

We used cotton thread as substrate to develop a novel room temperature DNA detection device for low-cost, sensitive and rapid detection of a human genetic disease, hereditary tyrosinemia type I related DNA sequences. A novel adenosine based molecular beacon (ABMB) probe modified on gold nanoparticle was used as reporter probe. In the presence of coralyne, a small molecule which can react with adenosines, the ABMB would form a hairpin structure just like traditional molecular beacon used extensively. In the presence of target DNA sequences, the hairpin structure of ABMB modified on gold nanoparticles will be opened and the biotin group modified at one end of the DNA probes will be released and react with the streptavidin immobilized on the test zone of the cotton thread. The response of the thread based DNA test device is linear over the range of 2.5-100 nM complementary DNA. The ability of our developed device for discriminating the single base mismatched DNA related to a human genetic disease, hereditary tyrosinemia type I, was improved comparing with previous report. It is worth mentioning that the whole assay procedure for DNA test is performed under room temperature which simplified the assay procedures greatly.

Polysaccharide purification from Haemophilus influenzae type b through tangential microfiltration.

Haemophilus influenzae type b (Hib) is a human pathogen that causes meningitis in infants worldwide. Capsular polysaccharide linked to a protein has been used as an efficient vaccine, and this approach has reduced the incidence of Hib disease since its inclusion in national immunisation campaigns. The traditional polysaccharide downstream process is based on several ethanol precipitations, treatment with detergents and centrifugation. The aim of this study was to introduce tangential microfiltration (TMF) in the place of centrifugation to simplify handling and to scale up the process. The purity of the polysaccharide was RPNA=1747.2 and RPPrt=196.1 for nucleic acid and protein, respectively, meeting the quality requirements for this polysaccharide. Moreover, the polysaccharide was recognised by at specific antibody, and the ribose and phosphate contents were within the expected limits. Thus, we established a process for the purification of capsular polysaccharide produced by H. influenzae type b that is effective, robust and feasible to be scaling up.

Protein from preprocessed waste activated sludge as a nutritional supplement in chicken feed.

Five groups of broiler chickens were raised on feed containing varying substitutions of single cell protein from preprocessed waste activated sludge (pWAS) in varying compositions of 0:100, 25:75, 50:50, 75:25, and 100:0 pWAS: fishmeal by mass. Forty chickens per batch were evaluated for growth rate, mortality rate, and feed conversion efficiency (ηє). The initial mass gain rate, mortality rate, initial and operational cost analyses showed that protein from pWAS could successfully replace the commercial feed supplements with a significant cost saving without adversely affecting the health of the birds. The chickens raised on preprocessed WAS weighed 19% more than those raised on fishmeal protein supplement over a 45 day test period. Growing chickens on pWAS translated into a 46% cost saving due to the fast growth rate and minimal death losses before maturity.

Development of a generic microfluidic device for simultaneous detection of antibodies and nucleic acids in oral fluids.

A prototype dual-path microfluidic device (Rheonix CARD) capable of performing simultaneously screening (antigen or antibody) and confirmatory (nucleic acid) detection of pathogens is described. The device fully integrates sample processing, antigen or antibody detection, and nucleic acid amplification and detection, demonstrating rapid and inexpensive "sample-to-result" diagnosis with performance comparable to benchtop analysis. For the chip design, a modular approach was followed allowing the optimization of individual steps in the sample processing process. This modular design provides great versatility accommodating different disease targets independently of the production method. In the detection module, a lateral flow (LF) protocol utilizing upconverting phosphor (UCP) reporters was employed. The nucleic acid (NA) module incorporates a generic microtube containing dry reagents. Lateral flow strips and PCR primers determine the target or disease that is diagnosed. Diagnosis of HIV infection was used as a model to investigate the simultaneous detection of both human antibodies against the virus and viral RNA. The serological result is available in less than 30 min, and the confirmation by RNA amplification takes another 60 min. This approach combines a core serological portable diagnostic with a nucleic acid-based confirmatory test.

G-quadruplex as signal transducer for biorecognition events.

G-rich nucleic acid oligomers can form G-quadruplexes built by G-tetrads stacked upon each other. The basic building block of the G-quadruplexes is similar, but the formation of different quadruplex structures is highly responsive to the strand stoichiometry, strand orientation, guanine glycosidic torsion angle, connecting loops, and the metal coordination. Because of its structural variations and different functions, G-quadruplex applied in biorecognition events can function as a versatile signaling component. A variety of strategies that incorporate G-quadruplex have also been reported. In this review, we mainly discuss G-quadruplex as signal transducer from the following aspects for biorecognition events: analyte-induced G-quadruplex reconfiguration and fluorescence enhancement of small ligand; analyte-induced G-quadruplex reconstruction and formation of DNAzyme; Stimulus-responsive G-quadruplex refolding and manipulation of electron transfer; Stimulus-responsive G-quadruplex and its combination with nanopore systems; Small ligand-responsive G-quadruplex stabilization for drug screening; Nanomaterial-reponsive G-quadruplex reformation; Target-triggered continuous formation of G-quadruplex by DNA nanomachine. We have comprehensively described the recent progress in our labs and others. Undoubtedly, bioanalytical technology and nanotechnology based on G-quadruplex will continue to grow, leading to develop new diagnostics, therapeutics and drug development.

Silicon-nanowire-based CMOS-compatible field-effect transistor nanosensors for ultrasensitive electrical detection of nucleic acids.

We herein report the design of a novel semiconducting silicon nanowire field-effect transistor (SiNW-FET) biosensor array for ultrasensitive label-free and real-time detection of nucleic acids. Highly responsive SiNWs with narrow sizes and high surface-to-volume-ratios were "top-down" fabricated with a complementary metal oxide semiconductor compatible anisotropic self-stop etching technique. When SiNWs were covalently modified with DNA probes, the nanosensor showed highly sensitive concentration-dependent conductance change in response to specific target DNA sequences. This SiNW-FET nanosensor revealed ultrahigh sensitivity for rapid and reliable detection of 1 fM of target DNA and high specificity single-nucleotide polymorphism discrimination. As a proof-of-concept for multiplex detection with this small-size and mass producible sensor array, we demonstrated simultaneous selective detection of two pathogenic strain virus DNA sequences (H1N1 and H5N1) of avian influenza.

Modulation of microbial predator-prey dynamics by phosphorus availability: growth patterns and survival strategies of bacterial phylogenetic clades.

We simultaneously studied the impact of top-down (protistan grazing) and bottom-up (phosphorus availability) factors on the numbers and biomasses of bacteria from various phylogenetic lineages, and on their growth and activity parameters in the oligo-mesotrophic Piburger See, Austria. Enhanced grazing resulted in decreased proportions of bacteria with high nucleic acid content (high-NA bacteria) and lower detection rates by FISH. There was a change in the composition of the bacterial assemblage, whereby Betaproteobacteria were heavily grazed while Alphaproteobacteria and Cytophaga-Flavobacterium-Bacteroides were less affected by predators. Changes in bacterial assemblage composition were also apparent in the treatments enriched with phosphorus, and even more pronounced in the incubations in dialysis tubes (allowing relatively free nutrient exchange). Here, Betaproteobacteria became dominant and appeared to act as successful opportunistic competitors for nutrients. In contrast, Actinobacteria did not respond to surplus phosphorus by population growth, and, moreover, maintained their small size, which resulted in a very low biomass contribution. In addition, significant relationships between high-NA bacteria and several bacterial phylogenetic clades were found, indicating an enhanced activity status. By combining several single-cell methods, new insight is gained into the competitive abilities of freshwater bacteria from a variety of phylogenetic lineages under contrasting sets of bottom-up and top-down constraints.

Homogenous rapid detection of nucleic acids using two-color quantum dots.

We report a homogenous method for rapid and sensitive detection of nucleic acids using two-color quantum dots (QDs) based on single-molecule coincidence detection. The streptavidin-coated quantum dots functioned as both a nano-scaffold and as a fluorescence pair for coincidence detection. Two biotinylated oligonucleotide probes were used to recognize and detect specific complementary target DNA through a sandwich hybridization reaction. The DNA hybrids were first caught and assembled on the surface of 605 nm-emitting QDs (605QDs) through specific streptavidin-biotin binding. The 525 nm-emitting QDs (525QDs) were then added to bind the other end of DNA hybrids. The coincidence signals were observed only when the presence of target DNA led to the formation of 605QD/DNA hybrid/525QD complexes. In comparison with a conventional QD-based assay, this assay provided high detection efficiency and short analysis time due to its high hybridization efficiency resulting from the high diffusion coefficient and no limitation of temperature treatment. This QD-based single-molecule coincidence detection offers a simple, rapid and ultra sensitive method for genomic DNA analysis in a homogenous format.

Influence of top-down and bottom-up manipulations on the R-BT065 subcluster of beta-proteobacteria, an abundant group in bacterioplankton of a freshwater reservoir.

We studied the effects of nutrient availability and protistan grazing on bacterial dynamics and community composition (BCC) in different parts of the canyon-shaped Rímov reservoir (Czech Republic). The effects of protistan grazing on BCC were examined using a size fractionation approach. Water from the dam area with only bacteria (<0.8 microm), bacteria and heterotrophic nanoflagellates (<5 microm), or whole water were incubated in situ inside dialysis bags. Top-down or predator manipulations (size fractionation) were also combined with bottom-up or resource manipulations, i.e., transplantation of samples to the middle and upper inflow parts of the reservoir with increased phosphorus availability. Significant genotypic shifts in BCC occurred with transplantation as indicated by denaturing gradient gel electrophoresis. Using different probes for fluorescence in situ hybridization, we found that 10 to 50% of total bacteria were members of the phylogenetically small cluster of beta-proteobacteria (targeted with the probe R-BT065). These rod-shaped cells of very uniform size were vulnerable to predation but very fast growing and responded markedly to the different experimental manipulations. In all the grazer-free treatments, the members of the R-BT065 cluster showed the highest net growth rates of all studied bacterial groups. Moreover, their relative abundance was highly correlated with bacterial bulk parameters and proportions of bacteria with high nucleic acid (HNA) content. In contrast, increasing protistan bacterivory yielded lower proportions of R-BT065-positive and HNA bacteria substituted by increasing proportions of the class Actinobacteria, which profited from the enhanced protistan bacterivory.

Molecular biomarkers in drug development.

Arguably, the most immediately promising reverberation of the genomics era has been the application of biomarkers to drug development. The promise of applying biomarkers to early drug development is that they might aid in preclinical and early clinical decisions such as dose ranging, definition of treatment regimen, or even a preview of efficacy. Later in the clinic, biomarkers could be used to facilitate patient stratification, selection and the description of surrogate endpoints. Information derived from biomarkers should result in a better understanding of preclinical and clinical data, which ultimately benefits patients and drug developers. If the promise of biomarkers is realized, they will become a routine component of drug development and companions to newly discovered therapies.

Chromatographic and electrophoretic methods for Lingzhi pharmacologically active components.

Lingzhi is the Chinese name given to the Ganoderma family of mushrooms, which was considered the most valuable medicine in ancient China and was believed to bring longevity, due to its mysterious power of healing the body and calming the mind. Today, Lingzhi is still widely revered as a valuable health supplement and herbal medicine worldwide, as studies (mostly conducted in China, Korea, Japan and the United States) into the medicinal and nutritional values of Lingzhi revealed that it does indeed contain certain bioactive ingredients (such as triterpenes and polysaccharides) that might be beneficial for the prevention and treatment of a variety of ailments, including important diseases such as hypertension, diabetes, hepatitis, cancers, and AIDS. As research into the biological activities of Lingzhi, as well as the quality assurance and quality control of Lingzhi products, require the isolation/purification of active ingredients from Lingzhi, followed by subsequent analytical and/or preparative separations, the present review summarizes the various chromatographic and electrophoretic methods (as well as sample pretreatment methods) typically employed to achieve such extraction/separation procedures.