bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uses of site-specifically modified RNAs constructed by RNA ligation
Authors: Moore Melissa J , Query Charles C 
Published: November 2023

Abstract
Recent development of efficient methods for constructing site-specifically modified RN As, especially those longer than permitted by complete chemical synthesis, has opened up many new experimental avenues to researchers interested in protein:RNA interactions. These include the introduction of radioactive labels and photocross-linking reagents for detecting proteins or other RNAs that interact with a particular site of interest, and the introduction of functional group modifications for structure-function probing at single or multiple nucleotide positions.
Proteolytic Enzymes: Nomenclature And Classification
Authors: Barrett Alan J 
Published: November 2023

Abstract
A landmark in the development of any field of study is the appearance of a sound system of nomenclature and classification for the objects with which it deals. The introduction of the Linnaean system for naming and classifying organisms in the eighteenth century and the invention of a system of nomenclature for enzymes in the 1950s were such key events, and their value has been obvious. Both nomenclature and classification are vitally important for intonations handling, allowing people to communicate efficiently, knowing that they are talking about the same thing, and to store and retrieve information unambiguously. A good system will also serve to highlight important questions, and thus prompt new discoveries.
Mass Spectrometry Of Proteolysis-Derived Peptides For Protein Identification
Authors: Kuster Bernhard , Shevchenko Andrej , Mann Matthias 
Published: November 2023

Abstract
Proteolytic enzymes are used in biological mass spectrometry for countless purposes ranging from, e.g. the solubilization of membrane proteins to epitope mapping and protein conformational studies. In particular, proteases are indispensable tools for peptide mapping and protein primary structure elucidation. Until a few years ago, the latter application was usually performed either by N terminal sequencing via the Edman chemistry or by HPLC separation of peptide mixtures again followed by Edman sequencing. This type of analysis was quite time consuming and protein amounts in the order of 100 pmol were frequently needed for ‘ internal sequencing’ . However, only much lower amounts are frequently available from biochemical preparations involving multiple purification stages, thus more sensitive characterization techniques are needed. MS has gradually become a viable alternative to Edman sequencing and now generally offers superior performance. Sub-picomole amounts of peptides can routinely be detected and partially sequenced by MS. In addition, the molecular weight. as obtained by MS, is a highly characteristic physicochemical property of a peptide and can often be used for the identification of known proteins in sequence data bases without the need for generating any peptide sequence.
In vitro transcription and characterization of transcription factors
Authors: Cooney Austin J , Tsai, Sophia Y , Tsai Ming-Jer 
Published: November 2023

Abstract
Once a cis-element and transacting factor have been determined to be important for regulation of transcription of a gene, gel retardation, DNAase I footprinting, methylation interference analyses, and in vitro transcription assays are generally employed for characterization of a factor during purification. The majority of transcription factors are present in very low quantities within a cell, making purification long and arduous, and requiring large quantities of starting material. Thus, the initial characterization of the factor is undertaken with partially purified material. This permits elucidation of vital information about the factor, such as the molecular weight, subunit composition, and interactions, if any, with non-DNA binding factors, before complete purification of the factor (1). This information is mostly derived from analysis of data from a combination of in vitro transcription assays and chromatographic and electrophoretic techniques, which will be covered in this chapter.
Preparation of chromatin templates for transcription studies
Authors: Boyes Joan 
Published: November 2023

Abstract
Transcription in the eukaryotic nucleus takes place within a highly packaged chromatin environment. Both genetic and biochemical approaches have been used to investigate how this process differs from transcription of protein-free DNA in vitro. This chapter describes various methods by which chromatin templates are generated for biochemical studies and discusses the merits of these different templates for particular studies. The preparation of histones and mononucleosome templates is described in full experimental detail. Moreover, the use of mononucleosome templates as a model to investigate nucleosome disruption over promoters is discussed.
Virus isolation
Authors: Cann A J , Irving W 
Published: November 2023

Abstract
There are two reasons why the difficult, expensive, and potentially hazardous procedure of virus isolation may be undertaken. The first is for the diagnostic identification of agents associated with disease. The other is to enable some subsequent experimental manipulation of the virus to be performed, for example, to examine mechanisms of replication or to determine the effectiveness of potential antiviral strategies in vitro. The protocols described in this chapter are derived from those used in a routine diagnostic virology laboratory, where the aim of virus isolation techniques is to cultivate and identify viruses from a variety of different types of potentially infected biological material (Table 1). Culture of viruses in large quantities for further experimental study relies on exactly the same principles, that is, provision of a suitable cell substrate, inoculation with material known to contain viable virus, and incubation under appropriate conditions.
Antiserum production and monoclonal antibodies
Authors: McKeating J , Shotton C , Valeri M 
Published: November 2023

Abstract
Since 1975, when Kohler and Milstein first reported the immortalization of antibody-secreting cells by somatic cell hybridization, hybridoma technology has proved to be an invaluable tool in the isolation and characterization of a variety of intra- and extracellular antigens (1). The principle is to propagate a clone of cells from a single antibody-secreting B lymphocyte, so that a homogeneous preparation of antibody can be obtained in large quantities. Hybrid cells are formed by the fusion of B lymphocytes (isolated from the lymph nodes or spleen of immunized animals) with a B-cell tumour line, most commonly, from the same species. The resultant hybridoma, once selected for specificity, will secrete the required antibody and can be grown indefinitely. Monoclonal antibodies (mAbs) produced against specific virus antigens have been used extensively to define the structure, function of virus components, and their interaction with proteins of virus and host-cell origin. Furthermore, such mAbs can form the basis of assays for the diagnosis of virus infection. Viruses generally have a regular, repeated, surface structure, and their surface-expressed antigens generally have a critical role in the attachment of virus to the host cell. Hence, such antigens provide a prime target for the immune system, and antibodies produced in response to these antigens have the potential to neutralize virus infectivity. These antibody-antigen interactions
Plant virus culture
Authors: Rybicki E P , Lennox S 
Published: November 2023

Abstract
Plant viruses are distinct from other major host-related groupings of viruses, such as animal or bacterial viruses, in that they are mostly single-stranded messenger-sense ss(+)RNA viruses, and mostly have simple, non-enveloped virions. There are a large number of types of simple isometric viruses, such as the Bromoviridae, Tombusviridae, and Comoviridae, as well as a wide variety of flexuous filamentous or rodlike types with helical capsid symmetry, such as the Potyviridae, Closteroviridae, and Tobamoviruses (1). There are some exceptions, notably with virus families that span different groups. Thus there are the enveloped ss(-)RNA plant Rhabdoviridae and Bunyaviridae, and the naked isometric dsRNA-containing plant Reoviridae (all of which may replicate in insect vectors and in insect cell cultures); there are two distinct groups of naked isometric ssDNA viruses with circular genomes (Geminiviridae and Nanoviruses) and two distinct groupings of plant pararetroviruses (Caulimo viridae and Badnaviruses) (2). While plant viruses as a group may not be as generally labile as their animal counterparts, given fewer enveloped viruses, it may be seen that there is considerable diversity, meaning that culture methods and methods for purification are similarly diverse.
Packaging of segmented and non-segmented RNA virus genomes
Authors: Barr J , McCauley J W 
Published: November 2023

Abstract
The process of virus assembly describes the events by which the mature virion is formed from its constituent components within an infected cell. Because viruses come in such a wide variety of structural arrangements and consequently have adopted incredibly diverse assembly strategies, this definition is by necessity very broad. The range of processes included in this term ‘assembly’ are extremely varied and range from simple associations of a genome with no more than a few types of protein (Tobacco Mosaic Virus, TMV, or X174) to the formation of a virion comparable in size to a small bacterium and containing over 100 different proteins (poxviruses). A detailed description of assembly is beyond the scope of this chapter, or indeed this book, and so the reader wishing to know more about the various assembly strategies adopted
X-ray crystallographic studies of protein-ligand interactions
Authors: Palmer Rex A 
Published: November 2023

Abstract
This chapter is concerned with current methods employed for the X-ray analysis of protein structures complexed with ligands. It deals with the methods used for growing crystals, the background to the use of X-ray intensity data, collection and measurement of the X-ray data, methods for analysing and interpretation of the structures. Whilst emphasis is given to the practical aspect of this type of work, in view of the highly specialized nature of X-ray crystallography it has been felt necessary to provide the reader with a background to the underlying theory. X-ray crystallography is highly computational and a great variety of software is available for performing the various stages of the calculations and graphics display. Some of the software used is specific to local research groups whilst other programmes are widely available and employed world-wide. Those programmes mentioned in the text are readily available and prospective users should have no difficulties obtaining copies complete with instructions. Important Internet addresses are included and major suppliers of specialised equipment are listed. The flow chart in Figure 1 indicates the various stages covered in the chapter.
Kinetics and thermodynamics of protein-protein interactions
Authors: Janin Joel 
Published: November 2023

Abstract
The physical chemistry of non-covalent protein-protein interactions aims to answer some fundamental questions: what is the origin of the affinity which enables biological macromolecules to form stable, complex, self-assemblies; what governs the specificity which makes these assemblies unique; which physical features give them functions that their individual components do not have? Given the ubiquitous character of protein-protein interactions, these questions are relevant to nearly all fields in biology, and they have attracted much interest over the years. An outline of the answer was given long ago by Linus Pauling and Max Delbrück (1):
Analysis and classification of protein-protein interactions from a structural perspective
Authors: Jones Susan , Thornton Janet M 
Published: November 2023

Abstract
Interactions between macromolecules are fundamental to many biological processes. Such interactions are central to the functioning of the vertebrate immune system, enzyme regulation, neurotransmitter release in the nervous system, and cell adhesion. The characterization of the interfaces formed when proteins interact is important if these and other systems are to be fully understood, and if the potential to control these interactions for medical and industrial applications is to be explored. The Brookhaven Protein Data Bank (PDB) (1, 2) now contains the three-dimensional coordinates of more than 12000 structures; an ever-increasing number of which are protein-protein complexes, including: oligomeric proteins; enzyme-inhibitor complexes; and antibody-protein complexes. Their deposition allows the analysis of large numbers of these structures, and such computational studies have provided important overviews of the physical and chemical properties of these associations (see, for example, refs 3-6). Protein-protein complexes with different interaction histories and functions require different modes of interaction. This chapter begins with the classification of these associations, considering functional classes of complexes, permanent and non-obligate complexes, and biological and crystallographic associations. The physical and chemical characteristics of biological associations are then discussed, presenting an overview of the properties favouring associations, namely hydrophobic and electrostatic interactions, and shape complementarity. These are then considered in more detail with reference to computational studies conducted on large data sets of protein complexes.
Functional genomics with yeast
Authors: Delneri Daniela , Oliver Stephen G 
Published: November 2023

Abstract
DNA sequencing and other biological data are accumulating at a vertiginous rate. Within the last 5 years, sequences of 23 prokaryotic genomes, the unicellular eukaryote Saccharomyces cerei1isiae (1), and the metazoan Caenorabditis elegans (2) were completed (Entrcz Genomes at The fission yeast Schizosaccharomyces pombe and the fruitfly Drosophila melanogasterwill be the next eukaryotes to have their genomes sequenced and released by the end of this year. There are about 70 microbial genomes (with sizes between 1.5-5 Mb) whose sequences are in progress. In autumn 1999, the first sequence of a human chromosome arm, 22p, was completed by an international consortium of sequencing centres (3). The Human Genome Project (HGP), which started at the beginning of the 1990s, should be completed in the next 5 years (4). By 2005, about 50years after the landmark paper of Watson and Crick on the structure of DNA (5), the complete description of all the genes contained in human chromosomes will be available. In parallel with the HGP, the mouse genome project has also been undertaken and is expected to be completed by 2008 (6).
Splicing pre-mRNA introns
Authors: Mayes Andrew E , Potashkin Judith A , Beggs Jean D 
Published: November 2023

Abstract
In the late 1970s it was discovered that many eukaryotic genes are interrupted by non-coding sequences (intrans). Since then, various types of intrans have been identified, the mechanisms for their removal have been intensively researched, and the possible reasons for their existence have been the subject of much debate. Introns are normally removed from newly transcribed RNA and the regions present in the mature RNA (exons) are concomitantly joined in a process termed RNA splicing. Three different chemical reactions of RNA splicing are currently known, exemplified by the splicing of 1) group I, 2) group II and nuclear precursor messenger RNA (pre-mRNA), and 3) tRNA introns (1). Genes containing group I intrans are found widely in nature, for instance in the chloroplast and mitochondria of plants, in mitochondria of fungi and other lower eukaryotes, in some eubacteria and bacteriophages. These introns have a characteristic, conserved secondary structure, and are spliced in a guanosine co-factor-dependent process that involves two trans-esterification reactions (2). Group II introns have been found in chloroplast, mitochondrial and some eubacterial genomes. They have a highly conserved secondary and tertiary structure that is distinct from that of group I introns. Group II introns (3) are spliced in how trans-esterification reactions that are very similar to those of pre-mRNA splicing (see below). However, unlike pre-mRNA splicing, which is dependent on a complex RNA- and protein-containing machinery called the spliceosome, some group I and group II introns have the ability to self-splice due to the autocatalytic activity of the RNA itself. In contrast to the first two types of splicing chemistry, tRNA introns are spliced in two distinct protein-catalysed reactions; first the intron is excised by an endonuclease, then the two exons are ligated (4).
RNA editing in Physarum polycephalum
Authors: Gott Jonathan M 
Published: November 2023

Abstract
RNAs synthesized in the mitochondria of the acellular slime mold, Physarum polycephalum, contain nucleotides which are not encoded, at least in the conventional sense, in the genes from which they are transcribed. These differences between the mitochondrial DNA and its mRNA (1–3), tRNA (4) and rRNA (5) products are due to multiple types of RNA editing. This topic has recently been reviewed in some detail (6), so the primary focus of this chapter will be on new developments in the field.
Paramyxovirus RNA polymerase stuttering
Authors: Hausmann StÉphane , Garcin Dominique 
Published: November 2023

Abstract
The concept of RNA editing was introduced in 1986 to describe the post-transcriptional insertion of non-genomically encoded uridylates within the coding region of trypanosome mitochondrial mRNAs, which restores the coding capacity of these genes (1). Many other examples of RNA editing by a variety of mechanisms, including nucleotide insertion, deletion and base substitution, were subsequently found. The term RNA editing now describes a large number of separate processes that produce RNA transcripts whose sequence (and informational capacity) differs from that encoded by the corresponding gene, excluding the alterations produced by splicing or 5’ and 3’ end formation (2–4).
Radioisotopes And Immunoassay
Authors: Bristow Adrian F , Thorpe Robin 
Published: November 2023

Abstract
Immunoassay is the quantitative measurement of a substance of interest (‘analyte’) using antibodies which bind specifically to that analyte. For the rest of this chapter, these two main components of the assay will be referred to as ligand and antibody respectively. In order to perform such an assay, it is necessary to measure the binding of the ligand to the antibody at very low concentrations; this has most commonly been achieved with the use of radioisotopes. The first practical application of the principle was the techniques of radioimmunoassay (RIA), invented by Yalow and Berson in the late 1950s (1), for which the Nobel Prize was subsequently awarded. This technique, and subsequently developed related techniques such as immunoradiometric assays and enzyme-linked immunosorbent assays, have revolutionized the biological sciences. Using these methods the minute quantities found in biological materials of a whole range of analytes such as protein hormones, steroids, viral antigens, cytokines and clotting factors can be accurately measured without relying on difficult and sometimes imprecise measurements based on their biological activities. Indeed, it is hard to overestimate the impact that the development of immunoassays has had on the life sciences.
Federal Regulations On Use Of Radionuclides In The USA
Authors: Hotte Eileen D , Nelson Neal 
Published: November 2023

Abstract
The use of radioactive materials and radiation-emitting devices in the USA is regulated by a number of agencies. In 1967, The World Health Organization re-ported that regulation of devices and materials emitting ionizing radiation was divided among 50 state governments, several city governments, six federal agencies, a Federal Council and a Federal Commission (1). The situation in the early 2000s is not much different. In the USA, regulation is by laws, statutes, standards, regulations and ordinances. Laws are the rules of conduct applied and enforced under the authority of state or federal government. They establish proper, permitted, denied and penalized behaviour and statements of goals or intent (2). Statutes are acts of legislature, administrative regulations or any enactment given the force of law by the state (2).
Web scripting for molecular biologists: An introduction to Perl and XML
Authors: Horton Robert M 
Published: November 2023

Abstract
Computer skills are increasingly important to molecular biologists. Internet literacy is essential for finding references in the literature (see Chapter 1), finding gene sequences from the databases (see Chapter 2), and many other tasks (as described in other chapters). Leaming how web-based programs work can help you to become a more effective user of these resources.
Minimal Invasive Versus Open Surgery for Colorectal Liver Metastases: A Multicenter German StuDoQ|Liver Registry-Based Cohort Analysis in Germany
Authors: Moosburner Simon , Kettler Chiara , Hillebrandt Karl H. , Blank Moritz , Freitag Hannes , Knitter Sebastian , Krenzien Felix , Nevermann Nora , Sauer Igor M. , Modest Dominik P. , Lurje Georg , Öllinger Robert , Schöning Wenzel , Werner Jens , Schmeding Maximilian , Pratschke Johann , Raschzok Nathanael ,   members of StuDoQ|Liver of Deutsche Gesellschaft für Allgemein- und Viszeralchirurgie/StuDoQ
Published: November 2023

Objective:
To compare the outcome of minimally invasive liver surgery (MILS) to open liver surgery (OLS) for resection of colorectal liver metastases (CRLM) on a nationwide level.

Background:
Colorectal cancer is the third most common malignancy worldwide. Up to 50% of all patients with colorectal cancer develop CRLM. MILS represents an attractive alternative to OLS for treatment of CRLM.

Methods:
Retrospective cohort study using the prospectively recorded German Quality management registry for liver surgery. Propensity-score matching was performed to account for variance in the extent of resection and patient demographics.

Results:
In total, 1037 patients underwent liver resection for CRLM from 2019 to 2021. MILS was performed in 31%. Operative time was significantly longer in MILS (234 vs 222 minutes, P = 0.02) compared with OLS. After MILS, median length of hospital stay (LOS) was significantly shorter (7 vs 10 days; P < 0.001). Despite 76% of major resections being OLS, postoperative complications and 90-day morbidity and mortality did not differ. The Pringle maneuver was more frequently used in MILS (48% vs 40%, P = 0.048). After propensity-score matching for age, body mass index, Eastern Cooperative Oncology Group, and extent of resection, LOS remained shorter in the MILS cohort (6 vs 10 days, P < 0.001) and operative time did not differ significantly (P = 0.2).

Conclusion:
MILS is not the standard for resection of CRLM in Germany. Drawbacks, such as a longer operative time remain. However, if technically possible, MILS is a reasonable alternative to OLS for resection of CRLM, with comparable postoperative complications, reduced LOS, and equal oncological radicality.