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Author congratulates David Gems and co-authors on a brilliant discovery — direct proof of acute phenoptosis in the nematode — but argues that the authors underappreciate the significance of their work by suggesting that phenoptosis is a rare natural phenomenon not typically observed in mammals. [ABSTRACT FROM AUTHOR]

Various used paper materials have been exposed to the action of cellulases from Penicillium funiculosum, Trichoderma reesei, Trichoderma viride and Aspergillus niger. A 2 h incubation period showed cellulase from T. viride the most active except for office paper that was maximally degraded by A. niger cellulase. Cellulase mixtures increased saccharification while sequential treatment with cellulases from T. reesei and P. funiculosum increased biodegradation at values between 15% and 190%. The maximum increase of saccharification (190%) was obtained when T. reesei cellulase initiated the sequential treatment of newspaper relative to the sole action of P. funiculosum cellulase on this non-pretreated and pretreated material. [ABSTRACT FROM AUTHOR]

The methodology used for analyzing the survival process should keep in mind heterogeneity in empirical data. Cross-sectional data are more heterogeneous in comparison with birth-cohort data. [ABSTRACT FROM AUTHOR]

Culture conditions for the production of cellulase-free endo-β-1,4-xylanase by an alkalophilic strain of Bacillus subtilis SD8 (BsSD8-xylanase) isolated from paper mill effluent were optimized using 2 factorial design and response surface methodology. Statistical analysis of results showed that the linear and quadratic terms and interaction of 4 variables (temperature, pH, inoculum size and xylan concentration) had significant effects. The optimal conditions for production of the enzyme were: 37.5°C, initial pH of 8.5, inoculum size of 8.5% and xylan concentration of 2%. The predicted and verified BsSD8-xylanase activities under optimal conditions were 8.18 IU/mL. Analysis revealed that the enzyme gene consists of an ORF of 642 bp encoding a protein of 213 amino acids with a molecular mass of 23.5 kDa and pI of 9.67. Secondary and tertiary structure prediction using SOPMA and SWISS model showed a maximum homology of 95.14% with β1,4-xylanase (PDB Id.: 1BVV) of Bacillus circulans obtained from protein data bank. The results of the study indicate that this enzyme presents a potentially effective xylan-biodegrading tool that could be useful for pulp and paper biobleaching. [ABSTRACT FROM AUTHOR]

At the Washington DC Pharmacogenomics in Drug Development and Regulatory Decision-Making: Workshop III – Three Years of Promise, Proposals and Progress on Optimizing the Benefit/Risk of Medicines (11–13 April 2005), one break-out session (Track 2) focused on co-development of therapeutic drug and diagnostic products. The Food and Drug Administration (FDA) released a draft concept paper shortly before the workshop was to convene. Track 2 was a forum for initial discussion of the content of the concept paper, and industry's initial reactions. After the workshop, formal commentaries on the co-development concept paper were submitted by several trade associations (e.g., Pharmaceutical Research and Manufacturers of America (PhRMA), Advanced Medical Technology Association (AdvaMed), American Association for Clinical Chemistry) and individual companies to FDA's Docket No. 2004N-0279. This paper includes a summary of the key features of the draft concept paper, the discussion in Track 2 of the April, 2005 meeting and highlights of the industry comments submitted to the FDA docket following the meeting.The Pharmacogenomics Journal (2006) 6, 375–380. doi:10.1038/sj.tpj.6500392; published online 2 May 2006 [ABSTRACT FROM AUTHOR]

Many important biochemical processes occur on the time-scales of nanoseconds and microseconds. The introduction of the laser temperature-jump (T-jump) to biophysics more than a decade ago opened these previously inaccessible time regimes up to direct experimental observation. Since then, laser T-jump methodology has evolved into one of the most versatile and generally applicable methods for studying fast biomolecular kinetics. This perspective is a review of the principles and applications of the laser T-jump technique in biophysics. A brief overview of the T-jump relaxation kinetics and the historical development of laser T-jump methodology is presented. The physical principles and practical experimental considerations that are important for the design of the laser T-jump experiments are summarized. These include the Raman conversion for generating heating pulses, considerations of size, duration and uniformity of the temperature jump, as well as potential adverse effects due to photo-acoustic waves, cavitation and thermal lensing, and their elimination. The laser T-jump apparatus developed at the NIH Laboratory of Chemical Physics is described in detail along with a brief survey of other laser T-jump designs in use today. Finally, applications of the laser T-jump in biophysics are reviewed, with an emphasis on the broad range of problems where the laser T-jump methodology has provided important new results and insights into the dynamics of the biomolecular processes. [ABSTRACT FROM AUTHOR]

Anaerobic fermentation converts organic waste into valuable products like volatile fatty acids (VFA). However, this process has weaknesses, such as delayed mass transfer, a slow microbe growth rate, poor hydrolysis, and surface heterogeneity. Such issues can be addressed by adding nanomaterials because they have unique physicochemical properties, such as a large surface area, many active sites, a high level of reactivity, a high level of specificity, the ability to self-assemble, and better mobility. This review focuses on the current efforts to investigate the effects of nanomaterials on improving VFA production. In addition, this work includes bibliometric information to aid in understanding current trends in this field of study. Furthermore, this work also reviewed the cytotoxicity and ecotoxicity of nanoparticles, followed by the applications and downstream processing of VFA. Finally, this paper discusses the reuse and recovery of several nanomaterials and provides a cost analysis. [ABSTRACT FROM AUTHOR]

Biochemical sensors have important applications in biology, chemistry, and medicine. Nevertheless, many biochemical sensors are hampered by intricate techniques, cumbersome procedures, and the need for labeling. In the past two decades, it has been discovered that liquid crystals can be used to achieve the optical amplification of biological interactions. By modifying recognition molecules, a variety of label-free biochemical sensors can be created. Consequently, biochemical sensors based on the amplification of liquid crystals have become one of the most promising sensors. This paper describes in detail the optical sensing principle of liquid crystals, sensing devices, and optical detection technologies. Meanwhile, the latest research findings are elucidated. Finally, the challenges and future research directions are discussed. [ABSTRACT FROM AUTHOR]

Discusses about concepts and theories on the biology and mechanism of aging. Impact of the introduction of molecular biology and gene engineering methods into life sciences on aging theories; Consideration of central nervous system as the initial substrate for aging; Role of telomeres and telomerase in basic processes underlying the fate of cells and whole organisms in terms of aging and death.

This article compares common methods of xenobiotic toxicity testing in earthworms including the filter paper contact method and the laboratory soil exposure method. Bioaccumulation of the pesticide Malathion was measured in Lumbricus terrestris along with clinical signs of toxicity in both methods. The authors argue that the two methods are not interchangeable and soil exposures may give more realistic results. They conclude that filter paper assays may be used as a rapid screening method for highly toxic chemicals but they tend to overestimate body burdens in exposed earthworms and should not be used when an environmentally realistic assessment is needed.

Two genome duplications early in the vertebrate lineage expanded gene families, including GluN2 subunits of the NMDA receptor. Diversification between the four mammalian GluN2 proteins occurred primarily at their intracellular C-terminal domains (CTDs). To identify shared ancestral functions and diversified subunit-specific functions, we exchanged the exons encoding the GluN2A (also known as Grin2a) and GluN2B (also known as Grin2b) CTDs in two knock-in mice and analyzed the mice's biochemistry, synaptic physiology, and multiple learned and innate behaviors. The eight behaviors were genetically separated into four groups, including one group comprising three types of learning linked to conserved GluN2A/B regions. In contrast, the remaining five behaviors exhibited subunit-specific regulation. GluN2A/B CTD diversification conferred differential binding to cytoplasmic MAGUK proteins and differential forms of long-term potentiation. These data indicate that vertebrate behavior and synaptic signaling acquired increased complexity from the duplication and diversification of ancestral GluN2 genes. [ABSTRACT FROM AUTHOR]

The article discusses the unidentified factors that caused the nitrogen (N)[2]) loss in the oceans. According to oceanographers it was virtually caused by denitrification, while investigators in the Netherlands, Germany and Denmark have revealed an additional biochemical called ammonia oxidation or anammox that produces N[2] in ocean waters. Meanwhile, Europeans showed that annamox in the absence of denitrification, accounted for most N[2] generation.

The article reports on the research conducted by David Bartel and Nikolaus Rajewsky regarding the implication of RNA to the production of cellular proteins in the U.S. When both intellectuals presented their work during the molecular biology symposium in Miami, they discovered that they were tackling the same issue. To unveil the mystery behind these cellular proteins, they need to look at changes in thousands of proteins at once and detect the differences in protein abundance. They found a glean insight into how miRNA act to fine tune the levels of thousands of proteins in a cell.

A convenient method for Knoevenagel and Nitroaldol condensation has been developed by using the inexpensive and environmentally friendly reagent I2/K2CO3 at room temperature in aqueous medium. The reaction condition is mild and simple with good to high product yields for both Knoevenagel as well as Nitroaldol condensation. [ABSTRACT FROM AUTHOR]

The article presents a guideline for contributors in the submission of papers to the "Pharmaceutical Chemistry Journal." It is indicated that the papers must contain recent investigations executed at a modern scientific way in fields like molecular biology and biochemistry and other technological experiments and ecological innovations.

The article presents information for the contributors of the journal "Khimiko Farmatsevticheskii Zhurnal". The papers submitted to the journal should reflect new, previously unreported investigations performed at the modern scientific and technological level and advanced commercial experience, in the fields of molecular biology and biochemistry. Papers presenting the results of experiments on the synthesis of new compounds and their characterization should contain separate chemical and biological experimental parts. Papers presenting new medicinal products should provide data on the chemical and physical properties; molecular and structural formulas; main results of the biological tests and clinical investigations.

The article presents instructions for the authors who contribute their papers to the journal "Biotechnology Letters." All relevant aspects of genetics and cell biochemistry, of process and reactor design, of pre- and post-treatment steps, and of manufacturing or service operations are accepted by the journal. Contributions from industrial and academic laboratories are equally welcome. Criteria for the acceptance of papers relate to the journal's aim of publishing useful and informative results that will be of value to other workers in related fields.

Porin of Haemophilus influenzae type b (341 amino acids; M(r) 37782) determines the permeability of the outer membrane to low molecular mass compounds. Purified Hib porin was subjected to chemical modification of lysine residues by succinic anhydride. Electrospray ionization mass spectrometry identified up to 12 modifications per porin molecule. Tryptic digestion of modified Hib porin followed by reverse phase chromatography and matrix assisted laser desorption ionization time-of-flight mass spectrometry mapped the succinylation sites. Most modified lysines are positioned in surface-located loops, numbers 1 and 4 to 7. Succinylated porin was reconstituted into planar lipid bilayers, and biophysical properties were analyzed and compared to Hib porin: there was an increased average single channel conductance compared to Hib porin (1.24 +/- 0.41 vs. 0.85 +/- 0.40 nanosiemens). The voltage-gating activity of succinylated porin differed considerably from that of Hib porin. The threshold voltage for gating was decreased from 75 to 40 mV. At 80 mV, steady-state conductance for succinylated porin was 50-55% of the instantaneous conductance. Hib porin at 80 mV showed a decrease to 89-91% of the instantaneous current levels. We propose that surface-located lysine residues are determinants of voltage gating for porin of Haemophilus influenzae type b. [ABSTRACT FROM AUTHOR]

It is widely accepted that ubiquitin-conjugating enzymes contain an active site asparagine that serves as an oxyanion hole, thereby stabilizing a negatively charged transition state intermediate and promoting ubiquitin transfer. Using structural and biochemical approaches to study the role of the conserved asparagine to ubiquitin conjugation by Ubc13-Mms2, we conclude that the importance of this residue stems primarily from its structural role in stabilizing an active site loop. [ABSTRACT FROM AUTHOR]

The bcl-2 protein plays an essential role in preventing cell death. Its activity is regulated through association with bcl-2 homologous and nonhomologous proteins and also by serine phosphorylation. We now report that bcl-2 can be proteolytically cleaved towards its N-terminus by a cysteine proteinase present in RL-7 lymphoma cell lysates, yielding a major product of apparent MW 20 kDa, different from the products of bcl-2 cleavage by HIV protease. Moreover, bcl-2 proteins mutated for Asp residues at positions 31 and 34 were efficiently cleaved by RL-7 cell lysates, indicating that this proteolytic activity is distinct from the caspase-3 that cleaves bcl-2 at Asp 34. This bcl-2 cleaving activity is inhibited by E-64 and is therefore distinct from the proteinases of the ICE/Ced-3 family (caspases), whereas reciprocally, ICE (caspase-1) is unable to cleave bcl-2. It is optimally active at pH 5, a feature distinguishing it from calpain, another non-ICE cysteine proteinase which has been associated with apoptosis. This novel bcl-2 cleaving protease, although constitutively present in RL-7 cells and resting peripheral blood lymphocytes (PBL) was upregulated following induction of apoptosis in RL-7 cells or mitogen activation in PBL. The N-terminus of bcl-2 which contains the BH4 domain that binds the kinase Raf-1 and the phosphatase calcineurin is essential for anti-apoptotic activity. Its cleavage might provide a novel post-translational mechanism for regulating bcl-2 function and could amplify ongoing programmed cell death. [ABSTRACT FROM AUTHOR]

The article focuses on the rapid publication of authors' results for primary journal dedicated to biotechnology. All relevant aspects of genetics and cell biochemistry, of process and reactor design, of pre- and post-treatment steps, and of manufacturing or service operations are included in the publication.

The paper discusses the core ideas and the development of biogeochemistry as an integrated research avenue in geochemistry and biology created by V.I. Vernadsky. Much attention is paid to the key concepts of biogeochemistry: living matter, the biogenic migration of chemical elements, and the chemical elemental composition of organisms and its ecological significance. The development of the various functions of the biosphere is analyzed: ecological, concentrational, and informational. The differentiation of the chemical elemental composition of organisms is analyzed under conditions when the biosphere is impacted by anthropogenic activities (the development of industries). The role of biogeochemistry is demonstrated with reference to the development of biotechnologies and the elaboration of a biogeochemical indication of the ecological state of biospheric taxons. The progress in biogeochemistry and its current problems are briefly analyzed. [ABSTRACT FROM AUTHOR]

The article focuses on "Biogeochemistry" periodical's creation of a section titled "Synthesis and Emerging Ideas" to fix a historical imbalance in the publication of science. Methods and data are published in journals where they both widely available and credited. Besides undermining and undervaluing the publication of ideas, this will potentially inhibit younger scientists from writing paper. With increasing electronic access to scientific literature, it has become increasingly important to provide more accessible and credible outlets for important synthesis and theoretical papers. The periodical wants to see the papers and advance the concepts involved in biogeochemistry, that will challenge and expand people's thinking and that will therefore lead to developing new tools and information.

Enzyme activity as a method for soil biochemistry and microbiology research has a long history of more than 100 years that is not widely acknowledged in terms of adherence to strict assay protocols and the interpretation of results. However, in the recent past, there is a growing lack of recognition of the historic advancements among researchers that use soil enzymology. Today, many papers are being published that use methods that either do not follow exact protocols as originally vetted in the research literature or individual labs use their own method that has not been optimized for pH, co-factors, substrate concentrations, or other conditions. This is of particular concern for fluorogenic substrates and microplate methods. Furthermore, there is a lack of understanding of the origin and location of a given enzyme being studied. Notably, regardless of the enzyme, it is too often assumed that enzyme activity equals microbial activity-which is not the case for most hydrolytic enzyme assays. Because as established by Douglas McLaren in the 1950s, a considerable amount of activity can come from catalytic enzymes stabilized in the soil matrix but that are no longer associated with viable cells (known as abiontic enzymes). In summary, today, many papers are using imperfect methods and/or misinterpret enzyme activity data that at a minimum confounds cross paper studies and meta-analysis. However, most importantly, lack of historical perspectives and ignoring strict protocols cause redundancy and fundamentally undermine the discipline and understanding of soil microbiology/biochemistry when enzymology methods are used. [ABSTRACT FROM AUTHOR]

The new competency-based medical education undergraduate curriculum (CBMC) was launched for the 2019 admission batch of MBBS students. The programme is designed to create an "Indian Medical Graduate" (IMG) possessing the requisite knowledge, skills, attitudes, values and responsiveness, so that the graduate may function appropriately and effectively as a physician of first contact with the community while being globally relevant. Given that implementation of this curriculum is still in its infancy across the country, we stand to gain from a unified approach to its implementation. Phase I of the curriculum includes anatomy, physiology, and biochemistry along with professional and personal development modules. Biochemistry enjoys an enviable position in the medical curriculum as it explains the molecular basis of diseases. We present an appraisal of the curriculum in Biochemistry by reviewing the components against Harden's six themes which are considered when planning or developing a curriculum. Further, five core components of CBME are selected on the basis of three research papers to characterize underlying assumptions of CBME to suggest ways of logical implementation for achieving the competencies expected of the Indian Medical Graduate. The insight gained shall help students to be equipped with competencies which they shall be able to use in their day- to- day work, which shall ultimately help benefit patient care and the society at large. [ABSTRACT FROM AUTHOR]

This paper shows a novel approach and a new model to find the relation of formulas between the thermodynamic parameters and electromagnetic parameters, directly and indirectly. Effectiveness of formulas is discussed by considering issues: no thermoregulation process (including body metabolism), no heat transfer consideration, and the Heating loss has not occurred and boundary conditions in a closed system. The enthalpy, internal energy, and Gibbs free energy are perfect indicators for describing bio-reaction in the human body. Because they are state functions (they are independent of intermediate steps, just first and final steps), they are affected by the SAR estimation that represents the absorption power throughout human tissue. These formulas brought in many features to control body reactions or Krebs cycle. Moreover, the derived formulas convert the reaction from non-spontaneous to spontaneous form by converting Gibbs free energy to a negative value. According to findings, the model can be applied in across many disciplines, such as medical treatment, lipid decomposition, cancer healing, and physical therapy. And in the end, as a result of an increase in the concentration of electromagnetic waves in the atmosphere due to technological development, which urges urgently to amend and update all equations to take into account the effect of magnetic waves in all disciplines affected by them. [ABSTRACT FROM AUTHOR]

This article presents information related to research conducted on soil and plant interactions. The article makes specific reference to publication of such researches in the periodical "Plant & Soil." Soil, It is stated that soil-plant interactions represent one of the most exciting challenges of scientific endeavors of the present century covering an array of topics ranging from chemistry to molecular biology, and from rhizosphere to ecosystems. It is highlighted that agriculture-oriented studies worldwide focused their attention on soil-plant interactions.

Franklin was no victim in how the DNA double helix was solved. An overlooked letter and an unpublished news article, both written in 1953, reveal that she was an equal player. [ABSTRACT FROM AUTHOR]

The giant anteater (Myrmecophaga tridactyla) is classified as a vulnerable species but is commonly received in rescue centers and zoos. Establishing hematological and biochemical reference intervals of free-ranging animals is an important tool to assess the health of both captive and wild populations. Reference values for 53 free-ranging giant anteaters in the Cerrado savanna of Mato Grosso do Sul state were established and differences across sexes and age groups were tested. Significant differences (p ≤ 0.05) between age groups (juvenile and adult) were found for hematocrit, mean corpuscular hemoglobin concentration (MCHC), lymphocytes, monocytes, platelets, total protein, globulin, alkaline phosphatase (ALP), glutamyl transpeptidase (GGT), and phosphorus. Between sexes, the only value that showed a significant difference was platelets. The data from the present study were also compared with previous studies and a worldwide zoological databank (ZIMS). White blood cell values were higher in all the studies with free-ranging giant anteaters compared to captive individuals. The relative eosinophils reference interval from our study was the highest ever reported for the species. This paper is the first published study with biochemical values for free-ranging giant anteaters and provides important reference intervals for future giant anteater in situ and ex situ conservation initiatives and highlights the importance of more veterinary research with comparative aspects between wild and captive animals. [ABSTRACT FROM AUTHOR]

Summary: Kew's Jodrell Laboratory was established in 1876 as a centre for botanical research in disciplines including plant physiology, anatomy and embryology, palaeobotany and mycology. Despite relatively little available funding, its location in one of the world's largest botanic gardens and close to several well-curated plant collections has ensured its continued existence for almost a century and a half. Under the far-sighted leadership of Kew's second Director, Joseph Dalton Hooker, the Jodrell Laboratory was established to coincide with Thomas Henry Huxley's pioneering course at the Normal School of Science in London. Funded by a generous private donation, the Laboratory complemented and augmented the programme in taxonomy and systematics already established in Kew's Herbarium, and provided a broader educational and research base to explore contemporary laboratory-based discoveries in fields such as physiology and lifecycles (sometimes termed the "New Botany"). The Jodrell Laboratory represents one of the world's first non-university affiliated laboratories and has spawned several "spin-off" facilities such as the Laboratory of Plant Pathology and the Millennium Seed Bank. This paper traces its early influence as an important centre for research in palaeobotany and plant systematics, its subsequent decline during the inter-war years, and a relatively dynamic period of innovative research following the construction of a new building on the same site. [ABSTRACT FROM AUTHOR]

Phytic acid (PA) is an abundant natural plant component that exhibits a versatility of applications benefited from its chemical structure, standing out its use as food, packing and dental additive due to its antimicrobial properties. The capacity of PA to chelate ions is also well-established and the formation and thermodynamic properties of different metallic complexes has been described. However, research studies of these compounds in terms of chemistry and biological features are still demanded in order to extend the application scope of PA complexes. The main goal of this paper is to deepen in the knowledge of the bioactive metal complexes chemistry and their bactericide activity, to extend their application in biomaterial science, specifically in oral implantology. Thus, this work presents the synthesis and structural assessment of two metallic phytate complexes bearing the bioactive cations Zn2+ and Sr2+ (ZnPhy and SrPhy respectively), along with studies on the synergic biological properties between PA and cations. Metallic phytates were synthesized in the solid-state by hydrothermal reaction leading to pure solid compounds in high yields. Their molecular formulas were C6H12024P6Sr4·5H2O and C6H12024P6Zn6·6H2O, as determined by ICP and HRES-TGA. The metal coordination bond of the solid complexes was further analysed by EDS, Raman, ATR-FTIR and solid 13C and 31P-NMR spectroscopies. Likewise, we evaluated the in vitro ability of the phytate compounds for inhibiting biofilm production of Streptococcus mutans cultures. Results indicate that all compounds significantly reduced biofilm formation (PA < SrPhy < ZnPhy), and ZnPhy even showed remarkable differences with respect to PA and SrPhy. Analysis of antimicrobial properties shows the first clues of the possible synergic effects created between PA and the corresponding cation in different cell metabolic processes. In overall, findings of this work can contribute to expand the applications of these bioactive metallic complexes in the biotechnological and biomedical fields, and they can be considered for the fabrication of anti-plaque coating systems in the dentistry field. [ABSTRACT FROM AUTHOR]

Abstract  In the current review paper the content of the journal Structural Chemistry for the calendar year 2008 is related to thermochemistry. Papers are summarized and a thermochemical slant added. Often questions are asked and research topics suggested. [ABSTRACT FROM AUTHOR]

Nanoporous gold made by dealloying AgAuPt (NPG-Pt) has been shown to exhibit several interesting catalytic properties, tied to its exceptionally high surface area; however, structural degradation may occur owing to thermal coarsening. To understand the effect of atmosphere chemistry on thermal coarsening and degradation, and means of limiting it, this study focuses on the high-resolution characterization of NPG-Pt layers coarsened in reductive Ar-H2 atmosphere, and in oxidative air. Atom probe tomography (APT) analysis is performed on NPG-Pt, coarsened separately in either Ar-H2 or air, to characterize the atomic-scale chemical changes in the nanoligaments and to develop a mechanistic view of the inherent processes. A tendency of Ag to segregate to the surface during coarsening is found to lead to complete elimination of the nanoligament core-shell structures in both cases. Large Pt segregates form during coarsening in Ar-H2, but under the surface of the ligaments, having relatively little effect on the coarsening rate. The oxygen-induced segregation of Pt was observed to cause the inhibition of thermal coarsening after minor loss in surface area-to-volume ratio. Findings in this paper help in understanding further the thermal coarsening of heterogeneous nanomaterials made by dealloying, and the pertinent factors that come into play in different chemical environments. [ABSTRACT FROM AUTHOR]

Cellulose-paper-based colorimetric bioassays may be used at the point of sampling without sophisticated equipment. This study reports the development of a colorimetric bioassay based on cellulose that can detect pathogen DNA. The detection was based on covalently attached single-stranded DNA probes and visual analysis. A cellulose surface functionalized with tosyl groups was prepared by the N, N-dimethylacetamide-lithium chloride method. Tosylation of cellulose was confirmed by scanning electron microscopy, Fourier transform infrared spectroscopy and elemental analysis. Sulfhydryl-modified oligonucleotide probes complementary to a segment of the DNA sequence IS 6110 of Mycobacterium tuberculosis were covalently immobilized on the tosylated cellulose. On hybridization of biotin-labelled DNA oligonucleotides with these probes, a colorimetric signal was obtained with streptavidin-conjugated horseradish peroxidase catalysing the oxidation of tetramethylbenzamidine by HO. The colour intensity was significantly reduced when the bioassay was subjected to DNA oligonucleotide of randomized base composition. Initial experiments have shown a sensitivity of 0.1 μM. A high probe immobilization efficiency (more than 90 %) was observed with a detection limit of 0.1 μM, corresponding to an absolute amount of 10 pmol. The detection of M. tuberculosis DNA was demonstrated using this technique coupled with PCR for biotinylation of the DNA. This work shows the potential use of tosylated cellulose as the basis for point-of-sampling bioassays. [ABSTRACT FROM AUTHOR]

In 1869, Johann Friedrich Miescher discovered a new substance in the nucleus of living cells. The substance, which he called nuclein, is now known as DNA, yet both Miescher's name and his theoretical ideas about nuclein are all but forgotten. This paper traces the trajectory of Miescher's reception in the historiography of genetics. To his critics, Miescher was a "contaminator," whose preparations were impure. Modern historians portrayed him as a "confuser," whose misunderstandings delayed the development of molecular biology. Each of these portrayals reflects the disciplinary context in which Miescher's work was evaluated. Using archival sources to unearth Miescher's unpublished speculations—including an analogy between the hereditary material and language, and a speculation that a series of asymmetric carbon atoms could account for hereditary variation—this paper clarifies the ways in which the past was judged through the lens of contemporary concerns. It also shows how organization, structure, function, and information were already being considered when nuclein was first discovered nearly 150 years ago. [ABSTRACT FROM AUTHOR]

Homeostasis occurs in a system where an output variable is approximately constant on an interval on variation of an input variable I . Homeostasis plays an important role in the regulation of biological systems, cf. Ferrell (Cell Syst 2:62–67, 2016), Tang and McMillen (J Theor Biol 408:274–289, 2016), Nijhout et al. (BMC Biol 13:79, 2015), and Nijhout et al. (Wiley Interdiscip Rev Syst Biol Med 11:e1440, 2018). A method for finding homeostasis in mathematical models is given in the control theory literature as points where the derivative of the output variable with respect to I is identically zero. Such points are called perfect homeostasis or perfect adaptation. Alternatively, Golubitsky and Stewart (J Math Biol 74:387–407, 2017) use an infinitesimal notion of homeostasis (namely, the derivative of the input–output function is zero at an isolated point) to introduce singularity theory into the study of homeostasis. Reed et al. (Bull Math Biol 79(9):1–24, 2017) give two examples of infinitesimal homeostasis in three-node chemical reaction systems: feedforward excitation and substrate inhibition. In this paper we show that there are 13 different three-node networks leading to 78 three-node input–output network configurations, under the assumption that there is one input node, one output node, and they are distinct. The different configurations are based on which node is the input node and which node is the output node. We show nonetheless that there are only three basic mechanisms for three-node input–output networks that lead to infinitesimal homeostasis and we call them structural homeostasis, Haldane homeostasis, and null-degradation homeostasis. Substantial parts of this classification are given in Ma et al. (Cell 138:760–773, 2009) and Ferrell (2016) among others. Our contributions include giving a complete classification using general admissible systems (Golubitsky and Stewart in Bull Am Math Soc 43:305–364, 2006) rather than specific biochemical models, relating the types of infinitesimal homeostasis to the graph theoretic existence of simple paths, and providing the basis to use singularity theory to study higher codimension homeostasis singularities such as the chair singularities introduced in Nijhout and Reed (Integr Comp Biol 54(2):264–275, 2014. 10.1093/icb/icu010) and Nijhout et al. (Math Biosci 257:104–110, 2014). See Golubitsky and Stewart (2017). The first two of these mechanisms are illustrated by feedforward excitation and substrate inhibition. Structural homeostasis occurs only when the network has a feedforward loop as a subnetwork; that is, when there are two distinct simple paths connecting the input node to the output node. Moreover, when the network is just the feedforward loop motif itself, one of the paths must be excitatory and one inhibitory to support infinitesimal homeostasis. Haldane homeostasis occurs when there is a single simple path from the input node to the output node and then only when one of the couplings along this path has strength 0. Null-degradation homeostasis is illustrated by a biochemical example from Ma et al. (2009); this kind of homeostasis can occur only when the degradation constant of the third node is 0. The paper ends with an analysis of Haldane homeostasis infinitesimal chair singularities. [ABSTRACT FROM AUTHOR]

The article reflects on the first paper anniversary of the "Nature Chemical Biology" publication. The periodical was launched with the aim of publishing topnotch research and commentary on biochemistry. Another goal is to raise international visibility of the field. More information is given in the article.

Biochemical reactions are often subject to a complex fluctuating environment, which means that the corresponding reaction rates may themselves be time-varying and stochastic. If the environmental noise is common to a population of downstream processes, then the resulting rate fluctuations will induce statistical correlations between them. In this paper we investigate how such correlations depend on the form of environmental noise by considering a simple birth-death process with dynamical disorder in the birth rate. In particular, we derive expressions for the second-order statistics of two birth-death processes evolving in the same noisy environment. We find that these statistics not only depend on the second-order statistics of the environment, but the full generator of the process describing it, thus providing useful information about the environment. We illustrate our theory by considering applications to stochastic gene transcription and cell sensing. [ABSTRACT FROM AUTHOR]

For a chemical reaction network, persistence is the property that no species tend to extinction if all species are initially present. We investigate the stronger property of vacuous persistence: the same asymptotic feature with a weaker requirement on initial states, namely that all species be implicitly present. By implicitly present, we mean for instance that if only water is present and the reaction network incorporates the information that water is made of hydrogen and oxygen, then hydrogen and oxygen are implicitly present. Persistence is inherently interesting and has implications for the global asymptotic stability of equilibrium states. Our main tools are the work of A. I. Vol'pert on the nullity and positivity of species concentrations, and the enabling notion of reachability. The main result states that a reaction network is vacuously persistent if and only if the set of all species is the only set of species that both is closed with respect to reachability and causes the implicit presence of all species. This paper is the first in a series of three articles. Two sequel papers introduce additional formalisms and use them to describe two large classes of reaction networks that are used as models in biochemistry and are vacuously persistent. [ABSTRACT FROM AUTHOR]

Fred Sanger, the inventor of the first protein, RNA and DNA sequencing methods, has traditionally been seen as a technical scientist, engaged in laboratory bench work and not interested at all in intellectual debates in biology. In his autobiography and commentaries by fellow researchers, he is portrayed as having a trajectory exclusively dependent on technological progress. The scarce historical scholarship on Sanger partially challenges these accounts by highlighting the importance of professional contacts, institutional and disciplinary moves in his career, spanning from 1940 to 1983. This paper will complement such literature by focusing, for the first time, on the transition of Sanger’s sequencing strategies from degrading to copying the target molecule, which occurred in the late 1960s as he was shifting from protein and RNA to DNA sequencing, shortly after his move from the Department of Biochemistry to the Laboratory of Molecular Biology, both based in Cambridge (UK). Through a reinterpretation of Sanger’s papers and retrospective accounts and a pioneering investigation of his laboratory notebooks, I will claim that sequencing shifted from the working procedures of organic chemistry to those of the emergent molecular biology. I will also argue that sequencing deserves a history in its own right as a practice and not as a technique subordinated to the development of molecular biology or genomics. My proposed history of sequencing leads to a reappraisal of current STS debates on bioinformatics, biotechnology and biomedicine. [ABSTRACT FROM AUTHOR]

The article provides information on a study about the calcium sensor approach that allows rapid and sensitive tracking of localized calcium signals with high temporal and spatial resolution. The researchers have presented a combination of tunability and small size of synthetic chemical indicators with the spatial resolution and control of genetically targeted proteins. Furthermore, they have developed a prototype small-molecule sensor, known as Calcium Green FlAsH in which it is comprised of receptor that binds selectively to calcium. Meanwhile, the author concludes that the researchers' general concept could be used to visualize protein regions by using methods other than fluorescence.

The increasing popularity of stable isotope analysis (SIA) as an ecological research tool and the ease of automated analysis have created a knowledge gap between ecologists using SIA and the operators of isotope ratio mass spectrometry (IRMS) equipment. This has led to deterioration in the understanding of IRMS methodology and its proper dissemination in the ecological literature. Of 330 ecological research papers surveyed, 63 (19%) failed to report any form of analytical error associated with IRMS. Of the 267 papers that reported analytical error, there was considerable variation both in the terminology and approach used to quantify and describe error. Internal laboratory standards were often used to determine the analytical error associated with IRMS, so chosen because they are homogenous and have isotopic signatures that do not vary over time. We argue that true ecological samples collected in the field are complex bulk mixtures and often fail to adhere to these two criteria. Hence the analytical error associated with samples is potentially greater than that of standards. A set of standard data run over time with a precision typically reported in the ecological literature (1 standard deviation: 1SD=0.26‰) was simulated to determine the likelihood of spurious treatment effects depending on timing of analysis. There was a 90% likelihood of detecting a significant difference in the stable nitrogen ratio of a single sample (homogenized bovine liver) run in two time periods when n>30. Minor protocol adjustments, including the submission of blind replicates by researchers, random assignment of sample repeats within a run by analytical labs, and reporting 1SD of a single sample analyzed both within and between runs, will only serve to strengthen the interpretation of true ecological processes by both researchers and reviewers. [ABSTRACT FROM AUTHOR]

This essay details a historical crossroad in biochemistry and microbiology in which penicillin was a co-agent. I narrate the trajectory of the bacterial cell wall as the precise target for antibiotic action. As a strategic object of research, the bacterial cell wall remained at the core of experimental practices, scientific narratives and research funding appeals throughout the antibiotic era. The research laboratory was dedicated to the search for new antibiotics while remaining the site at which the mode of action of this new substance was investigated. This combination of circumstances made the bacterial wall an ontology in transit. As invisible as the bacterial wall was for clinical purposes, in the biological laboratory, cellular meaning in regard to the action of penicillin made the bacterial wall visible within both microbiology and biochemistry. As a border to be crossed, some components of the bacterial cell wall and the biochemical destruction produced by penicillin became known during the 1950s and 1960s. The cell wall was constructed piece by piece in a transatlantic circulation of methods, names, and images of the shape of the wall itself. From 1955 onwards, microbiologists and biochemists mobilized new names and associated conceptual meanings. The composition of this thin and rigid layer would account for its shape, growth and destruction. This paper presents a history of biochemical morphology: a chemistry of shape - the shape of bacteria, as provided by its wall - that accounted for biology, for life itself. While penicillin was being established as an industrially-manufactured object, it remained a scientific tool within the research laboratory, contributing to the circulation of further scientific objects. [ABSTRACT FROM AUTHOR]

The paper introduces the dynamics of a stochastic multi-molecule biochemical reaction model.First, we show that there is a unique positive solution of the stochastic model. Furthermore, we deduce the conditions when the reaction will end and when the reaction being proceed. At last, we derive that the solution of (1.5) oscillates around the endemic proportion equilibrium $$P^*(x^*,y^*)$$ , and the intensity of fluctuation is proportional to white noise. The key to the analysis in this paper is choosing appropriate Lyapunov function. The outcomes are illustrated by computer simulations throughout this paper. [ABSTRACT FROM AUTHOR]

Biochemical mechanism studies often assume statistical models derived from Michaelis–Menten kinetics, which are used to approximate initial reaction rate data given the concentration level of a single substrate. In experiments dealing with industrial applications, however, there are typically a wide range of kinetic profiles where more than one factor is controlled. We focus on optimal design of such experiments requiring the use of multifactor hybrid nonlinear models, which presents a considerable computational challenge. We examine three different candidate models and search for tailor-made D- or weighted-A-optimal designs that can ensure the efficiency of nonlinear least squares estimation. We also study a compound design criterion for discriminating between two candidate models, which we recommend for design of advanced kinetic studies. Supplementary materials accompanying this paper appear on-line [ABSTRACT FROM AUTHOR]

In this paper, we incorporate stochastic incidence of a chemical reaction into the standard Keizer's open chemical reaction. We prove that a positive stationary distribution (PSD) for the associated chemical master equation exists and is globally asymptotically stable. We present threshold dynamics of the stochastic Keizer's model in term of the profile of the PSD for both finite and infinite volume size V. This establishes a sharp link between deterministic Keizer's model and the stochastic model. In this way, we resolve Keizer's paradox from a new perspective. This simple model reveals that such stochastic incidence incorporated, though negligible when V goes to infinity, may play an indispensable role in the stochastic formulation for irreversible biochemical reactions. [ABSTRACT FROM AUTHOR]

The story of how the structure of DNA was found is one of team science from which one member was unforgivably excluded. [ABSTRACT FROM AUTHOR]