bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation and purification of monoclonal antibodies from tissue culture supernatant
Authors: Hale Geoff 
Published: November 2023

Abstract
Why do you need to purify an antibody? There are many possible reasons and the answer will be a major factor in determining the best strategy. Depending on the intended application, different contaminants are important and different degrees of purity are necessary (Table 1). Manufacture of antibodies for human therapy imposes many stringent requirements which are beyond the scope of this chapter. Anyone intending to develop a process for ultimate therapeutic application should seek detailed advice at an early stage.
Antibody production in plants
Authors: Drake* Pascal , Stogert Eva , Nicholson Liz , Christout Paul , Ma Julian K C 
Published: November 2023

Abstract
Plant biotechnology is a rapidly expanding area and in the last five to ten years it has become apparent that plant systems may be particularly valuable for the expression and production of recombinant proteins such as pharmaceuticals, vaccines, and in particular, antibodies. A particular attraction of this approach is the potential for producing these kinds of reagents on an agricultural scale, thereby significantly reducing the costs of production. However there are also many other advantages related to the use of plants. In this chapter, we shall provide a brief review of the advances made in plant expression of antibodies and describe the principles of plant genetic engineering as well as the major techniques that are involved.
lmmunogold probes for light and electron microscopy
Authors: Monaghan Paul , Robertsont David 
Published: November 2023

Abstract
The characteristics of monoclonal antibodies make them particularly suitable for electron microscope (EM) immunolabelling studies. At the high magnifica tion of the EM, any non-specific labelling can be a real problem, and some of the best antibodies we have used are monoclonal antibodies. The principles of immunocytochemistry are essentially the same for both light and electron microscopy. A primary antibody is persuaded to bind to its antigen and this is then detected by a suitable marker. For electron microscopy, a number of mark ers have been used including ferritin and horseradish peroxidase/DAB reaction product. However colloidal gold is an almost perfect marker in this context and alternatives are rarely used. Colloidal gold is particulate and electron dense making it readily visible in the EM. In addition, it does not obscure the underly ing cellular structure, making it easy to localize antigens not just to specific organelles, but regions within these structures. Colloidal gold can be formed in defined sizes and this has implications for its use, particularly in multiple labelling experiments.
lmmunochemical detection of BrdUrd labelled nuclei for monitoring cell kinetics
Authors: Wilson George D 
Published: November 2023

Abstract
Cell kinetics is defined as the measurement of time parameters in biological systems. This chapter describes the use of BrdUrd/DNA flow cytometry to study cell kinetics of cells in culture. The technique involves pulse labelling with BrdUrd after which samples are then taken at time intervals thereafter. The cells are stained with a monoclonal antibody against BrdUrd and visualized by a secondary antibody conjugated to a fluorochrome (usually fluoroscein isothio cyanate, FITC) and counterstained with propidium iodide (Pl) to measure the DNA content, and analysed on the flow cytometer. The simultaneous measure ment of BrdUrd incorporation and DNA content confers sensitivity and versa tility in detection of cell cycle perturbations in response to drugs or radiation and tracing the lineage of a cell within the cell cycle. The speed and quantitative power of the flow cytometer, in conjunction with the specificity and sensitivity of monoclonal antibody techniques, provide the basis for the adoption and success of the BrdUrd technique in experimental and clinical investigations. The use of computer-generated windows facilitates the analysis of any population of cells within any phase of the cell cycle and is not restricted to the ‘mitotic window’, as previously was the case with HTdRfautoradiography.
Assay and purification of protein-serine/threonine kinases
Authors: Grahame Hardie D , Haystead Timothy A J , Salt Ian P , Davies Stephen P 
Published: November 2023

Abstract
It is now very clear that activation of protein kinase cascades (ably assisted by appropriate regulation of protein phosphatases) is the major mechanism by which eukaryotic cells respond to changes in the extracellular environ-ment, such as the presence of extracellular signal molecules or adverse envilronmental conditions. It also appears to be the major mechanism through which cellular processes which occur discontinuously (e.g. DNA replication, mitosis) are switched on and off. Although there are exceptions, protein kinases are usually expressed constitutively, and the key event is activation of pre-existing kinase protein, through phosphorylation, dephosphorylation, binding of an allosteric activator (e.g. cyclic AMP, 5’-AMP, Ca2+, diacylglycerol), or binding of a regulatory protein (e.g. a cyclin). It is therefore very important to develop methods to assay protein kinase activity. In some cases (e.g. MAP kinases) the activating phosphorylation produces a mobility shift on SDS-polyacrylamide gel electrophoresis (PAGE), and the activation can be assessed by Western blotting. However, non-activating phosphorylation events can also produce mobility shifts, and this method can be unreliable or misleading. There is, therefore, no real substitute for the development of direct assays of protein kinase activity. This is the first main topic of this chapter (see Section 2).
Techniques for elucidating the secretory process: from Ca2+ entry to exocytosis
Authors: Fisher Thomas e. , Oberhauser andres f. 
Published: November 2023

Abstract
Technical innovation has always been central to progress in the study of neurotransmission. The first demonstration of chemical neurotransmission was in fact made possible by a novel and ingenious experimental approach. In 1921 Otto Loewi rushed to his laboratory in the middle of the night to perform an experiment that had occurred to him in a dream. It had been known for some time that stimulation of the vagal nerve causes slowing of the frog heart. Loewi’s insight was to stimulate the vagus of a perfused frog heart and then add the perfusate to the solution bathing a second frog heart in a separate vessel. This caused the slowing of the second heart, demonstrating that the vagal action was caused by release of a chemical substance, later shown to be acetylcholine. From this simple, elegant beginning the techniques for studying neurotransmission have developed to the point where it is now possible to measure exocytosis at the level of a single neuron, with the precision to detect the fusion of a single synaptic vesicle with the neuronal membrane.
Sequence analysis of expressed proteins
Authors: Keen Jeff N , Ashcroft Alison E 
Published: November 2023

Abstract
The generation of recombinant proteins may be considered a relatively facile process nowadays. The wide range of expression systems available, and the marketing of specialized molecular biological kits by a number of manufacturers, virtually ensure that reasonable quantities of recombinant proteins can be produced in most biochemistry laboratories, although there are notable exceptions such as some integral membrane proteins. The engineering of appropriate ‘tags’ (e.g. hexa-His, StrepTag) into the DNA sequence encoding any particular protein frequently enables single-step affinity purification of the expressed polypeptide. Similarly, the creation of a fusion protein, with the desired polypeptide linked to glutathione S-transferase for example, allows ready expression and purification of the protein. The incorporation of a unique protease-sensitive site (e.g. for Factor Xa) into the linking region between the two polypeptide domains enables the desired product to be removed from the fusion protein. However, unequivocal proof of the identity of the expressed protein and detailed analysis of the synthetic fidelity are essential prerequisites for its use in experimental systems, particularly in structural and functional analysis, and are absolutely critical prior to release of the protein into the environment in numerous biotechnological applications. The confirmation of N- and C-termini is of paramount importance, and amino acid sequence analysis remains the most unambiguous technique for this. This is complemented by mass spectrometric methods, particularly utilizing electrospray ionization, for accurate mass measurement of the expressed protein. This in turn enables a comparison to be made with the theoretical value, which may indicate the presence of post-translational modifications and lead to their identification.
Protein degradation in mammalian cells
Authors: Ciechanover Aaron , Wiederanders Bernd 
Published: November 2023

Abstract
Recent experimental evidence implicates the ubiquitin system in the specific and programmed degradation of many key regulatory and short-lived cellular proteins. Among these are mitotic cyclins, transcriptional activators, tumour suppressors, and growth regulators, as well as membrane receptors involved in signal transduction and the immune and inflammatory responses. It is also involved in processing of antigens for presentation via class I MHC molecules. The system can specifically target abnormal, misfolded, and unassembled proteins that may result from mutations, environmental damage, or non stoichiometric synthesis of subunits of complex proteins. It is clear therefore that ubiquitin-mediated proteolysis plays important roles in the regulation of basic pathophysiological cellular processes such as regulation of cell cycle and division, development and differentiation, malignant transformation, modulation of the immune system, and neurodegeneration. With the multitude of substrates targeted, it is not surprising that recent studies have implicated the system in the pathogenesis of several disease states as well. For example, the inability to degrade the kidney Na+ channel leads to stabilization of the protein, accumulation of the channel subunits, excessive reabsorption of the cation and water, and a severe form of hypertension (1). Mutations in the gene that encodes E6-AP, a ubiquitin-protein substrate ligase, lead to the Angelman syndrome that is characterized by mental retardation, seizures, and abnormal gait (2). It is predicted that the list of ubiquitin-related pathological derangements will grow significantly in the future.
Epidemiological methods for studies of genetic factors that influence infectious diseases
Authors: Engels Eric A , O’Brien Thomas R 
Published: November 2023

Abstract
Epidemiological studies are concerned with the relationship within populations between exposures and outcomes. A strong relationship between an exposure and outcome provides evidence that the exposure, at least in part, is a cause of the outcome. Numerous types of exposures are of potential interest to epidemiologists. These types include, but are not limited to, environmental exposures (e.g. toxic chemicals or radiation), exposures defined by socioeconomic status or occupation (which can be markers for more specific exposures that are difficult to measure), and endogenous exposures (e.g. blood pressure or hormone levels). An additional type of exposure is provided by infectious agents, i.e. micro-organisms such as viruses, bacteria, or parasites. Infectious diseases, by definition, require exposure to an infecting organism for the development of disease. Nonetheless, although contact with the micro-organism is necessary for infectious diseases, it is often not sufficient. Not everyone who is exposed to an infectious organism becomes infected, and not everyone who becomes infected develops disease.
Introduction to the principles of flow cytometry
Authors: Carter Nigel P , Ormerodt Michael G 
Published: November 2023

Abstract
1 Introduction
Flow cytometry is a technique for making rapid measurements on particles or cells as they flow in a fluid stream one by one through a sensing point. The important feature of flow cytometric analysis is that measurements are made separately on each particle within the suspension in turn, and not just as average values for the whole population. The ability of laser- and arc lamp-based flow cytometers to measure multiple cellular parameters, based on light scatter and fluorescence, and to purify physically subpopulations of cells has led to the increasingly widespread use of this instrumentation in biology and medicine. The applications of flow cytometry and cell sorting are numerous. A wide range of fluorescent probes is available for directly estimating cellular parameters such as nucleic acid content, enzyme activity, calcium flux, membrane potential, and pH. Conjugation of fluorescent dyes to ligands and to polyclonal and mono clonal antibodies has enabled the density and distribution of cell-surface and cytoplasmic determinants and receptors to be studied, as well as allowing functional subpopulations of cells to be identified. Many of these fluorescent dyes and reagents can be used in combination to produce multiple correlated measurements. For example, it is now commonplace in immunology to measure two light-scatter and three immunofluorescence parameters on each cell.
Microinjection
Authors: Knoblauch Michael 
Published: November 2023

Abstract
During recent decades, microinjection has developed into an important method used by cell biologists, and there have been several thousand papers published describing applications of this technique. The main advantage of microinjection is that it enables the direct introduction of substances into individual cells or organelles whilst being observed. Microinjection can be used in intact tissue of whole plants as well as in tissue cultures or tissue slices. In essence, for micro injection a glass pipette (needle) with a tip size of about 1 µm is filled with the substance to be introduced. The substance is forced from the capillary by hydro static pressure (pressure injection) or by an electric current (iontophoresis) into the cell. The main problem is that the method is technically demanding. On the other hand, it is inexpensive, costs being mainly associated with purchase of the experimental hardware.
Patterning and Positional Information
Authors: Wolpert L , Kerszberg M 
Published: November 2023

Abstract
Pattern formation is a key process in embryonic development (1). When a fertilized egg divides, the resulting cells become different and give rise to a variety of structures such as the main body and its appendages. These structures have a well-defined spatial organization-the vertebrate limb is a good example—which is brought about by the process of pattern formation. There are three other related processes: (1) cell differentiation is the process by which different specialized adult cell types such as muscle, cartilage, and neurons are generated; (2) morphogenesis, or a change in form, such as neural tube formation; and (3) growth—it is a general feature of pattern formation that it is initially only specified for any organ on a small scale—rarely greater than more than 100 cell diameters. These processes are related to one another but, in general, pattern formation is the primary event in that it specifies the other processes. Thus patterning in vertebrate limb development specifies where cartilage will form and how it will grow; it also specifies ectodermal cells such as the apical ridge, which controls the overall form of the limb.
Narrow Roads Of Gene Land
Authors: Hamilton W D 
Published: November 2023

Abstract
Why is `blood thicker than water’? Are we innately violent or pacific? What is the best sex ratio? Why are plants and animals sexual? Why do we grow old and die? Over what do our chromosomes quarrel? Such questions have motivated the life-work of W.D. Hamilton, widely acknowledged as the most important theoretical biologist of the 20th century. His papers continue to exert an enormous influence and they are now being republished for the first time. Each one is introduced by an autobiographical essay written especially for this collection. This first volume contains all of Hamilton's publications prior to 1981, a set especially relevant to social behaviour, kinship theory, sociobiology, and the notion of `selfish genes'. It includes several of the most read and famous papers of modern biology. A forthcoming volume will be devoted to the second half of Hamilton's life's work, on sex and sexual selection. Narrow Roads of Gene Land will be welcomed by professionals, graduate students, and undergraduates from a variety of disciplines, including evolution, population genetics, animal behaviour, genetics, anthropology, and ecology. The essays are accessible to non-specialists and will fascinate and entertain general readers with an interest in evolution and behaviour.
Clinical utility of the forward-viewing echoendoscope in patients after pancreatoduodenectomy: A prospective study
Authors: Ishiwatari Hirotoshi , Kaneko Junichi , Sato Junya , Satoh Tatsunori , Ishikawa Kazuma , Niiya Fumitaka , Matsubayashi Hiroyuki , Minamide Tatsunori , Maeda Yuki , Yamamoto Youichi , Kishida Yoshihiro , Yoshida Masao , Ito Sayo , Kawata Noboru , Imai Kenichiro , Hotta Kinichi , Imamura Taisuke , Sugiura Teiichi , Uesaka Katsuhiko , Ono Hiroyuki 
Published: November 2023

ABSTRACT

Background and Objectives
Endoscopic treatment of obstructive jaundice and pancreatitis due to hepaticojejunostomy (H-J), pancreatojejunostomy (P-J) strictures, and tumor recurrence after pancreatoduodenectomy (PD) is technically challenging. Treatment of P-J strictures results in poor outcomes. Although conventional EUS that has an oblique view is not suitable for such patients, forward-viewing EUS (FV-EUS) may become a useful option. This study aimed to evaluate the feasibility and efficacy of FV-EUS in patients who have undergone PD.

Methods
Patients with PD who were scheduled to undergo diagnosis and treatment using FV-EUS for H-J or P-J lesions were enrolled in this single-center prospective study. After observation of the P-J and H-J using FV-EUS according to a predetermined protocol, treatment using FV-EUS was performed as needed.

Results
A total of 30 patients were enrolled, and FV-EUS was used to observe P-J and H-J in 24 and 28 patients, respectively. The detection rates of P-J and H-J by endoscopy were 50% (12/24) and 96.4% (27/28), respectively, and by EUS were 70.8% (17/24) and 100% (28/28), respectively. Of these, P-J and H-J were found by endoscopy only after EUS observation in 3 and 1 patient, respectively. The success rates of endoscopic treatment using FV-EUS were 66.7% (2/3), 95.2% (20/21), and 25% (1/4) for benign P-J strictures, benign H-J strictures, and tumor recurrence, respectively.

Conclusions
Endoscopic treatment using FV-EUS is feasible and effective for patients after PD. Moreover, FV-EUS increases the P-J lesion detection rate by adding EUS observation.
Feasibility of Surveillance for Mucinous Cystic Neoplasm of the Pancreas
Authors: Hozaka Yuto , Ohtsuka Takao , Nakamura Masafumi , Hijioka Susumu , Unno Michiaki , Shimizu Yasuhiro , Tanabe Minoru , Nagakawa Yuichi , Hatano Etsuro , Kawai Manabu , Sano Tsuyoshi , Koshita Shinsuke , Katanuma Akio , Kita Emiri , Hanada Keiji , Nakai Yousuke , Aoki Takeshi , Serikawa Masahiro , Okamoto Kojun , Takeyama Yoshifumi 
Published: November 2023

Objective
We aimed to elucidate the feasibility of surveillance of patients with mucinous cystic neoplasm (MCN).

Methods
We performed a retrospective, multi-institutional study of 328 patients who underwent surgery for MCN at 18 Japanese institutions. Patients with MCN were divided into an immediate surgery group and a surveillance group, which underwent surgery after surveillance.

Results
The median surveillance period until surgery in the surveillance group was 27 months (range, 7–165 months). Compared with the immediate surgery group, the surveillance group showed smaller tumor diameter (46 vs 50 mm, P = 0.01), more frequent laparoscopic approach (58% vs 37%, P < 0.01), and less frequent malignancy (7% vs 15%, P = 0.03). The new appearance of mural nodules and elevation of serum tumor markers were associated with malignancy in the surveillance group. Two patients in the surveillance group experienced postoperative recurrence, although there was no significant difference in recurrence or disease-free survival between the two groups. In the surveillance group, the 1-, 5-, and 10-year cumulative incidence rates of malignant MCN were 0.8%, 5.6%, and 36.5%, respectively.

Conclusion
As the risk of progression to malignant MCNs increases over the long term, MCNs should be resected rather than subjected to unnecessary surveillance.
Daily Pain Experiences in Chronic Pancreatitis
Authors: Han Samuel , Li Rui , Palermo Tonya M. 
Published: November 2023

Objectives
Pain, the hallmark symptom of chronic pancreatitis (CP), remains difficult to assess. To capture the variability of pain that patients can experience day to day, this study used pain diaries to describe daily pain experiences and identify pain phenotypes.

Methods
This study is a secondary data analysis from a pilot trial examining cognitive behavioral therapy for pain treatment in CP. Before treatment, patients completed an online daily pain diary using the Brief Pain Inventory for 7 days. Using indicators of pain magnitude, pain variability, pain synchrony along with least, worst, and average pain intensity levels, we identified pain patterns using K-means clustering.

Results
Of 30 patients in the pilot trial, a total of 27 patients (mean age of 49.8 years, 80% women) had complete data to include in this report. Four clusters were identified: cluster 1, lowest pain magnitude (n = 3); cluster 2, moderate pain magnitude and high pain variability (n = 4); cluster 3, moderate pain magnitude and low pain variability (n = 9); and cluster 4, highest pain magnitude and lowest pain variability (n = 11).

Conclusions
Daily pain diaries offer a novel way of evaluating the dynamic pain experiences in CP. Although 4 distinct pain patterns were identified, further studies are needed to validate these findings.