Index
A
A. nidulans, 478
Ab (antibody) macromodule, 34
Acid formers, in waste treatment, 564
Acidophiles, 14
Actinomycetes, 19
Activated-sludge processes, biological waste treatment, 551–553
Active cell immobilization, 298–302
Active sites, 63
Acylation, 115
ADC (adsorption chromatography), 410–411
ADC (antibody-drug conjugate), 36
Adenosine monophosphate (AMP), 45
Adenosine triphosphate (ATP). See ATP (adenosine triphosphate).
Adsorbent-added activated-sludge process, 557–558
Adsorption
ADC (adsorption chromatography), 410–411
enzyme immobilization, 87
Freundlich adsorption isotherm, 403–404
immobilized cell systems, 300–301
separation of soluble products, 403–409
Adsorption chromatography (ADC), 410–411
Adsorption zone, separation of soluble products, 405
Aeration, bioreactor scale-up, 331–337
Aerobic bioprocesses. See also Anaerobic bioprocesses.
baker’s yeast production, 588–590
citric acid production, 586–588
HFCS (high-fructose corn syrup) production, 593–595
penicillin production, 590–592
VEFCS (very enriched fructose corn syrup) production, 595
Aerobic organisms, 14
Aerobic respiration, glycolysis, 149
Aerotaxis, 138
AFC (affinity chromatography), 411, 414–419
Ag (antigen) macromodule, 34, 36
Aggregates in plant cell cultivation, 460
Agitation, bioreactor scale-up, 331–337
Agricultural wastes, biological waste treatment, 549
Airlift system, bioreactor scale-up, 329–330
Ajmalicine from periwinkle, 465
Aldehydes, 38
Algae
Chlorella, 27
definition, 27
Dunaliella, 27
microscopic eucaryotes, 27
Scenedesmus, 27
size, 27
Spirulina, 27
Alkaliphiles, 14
Alkylation, 116
Ameboid motion, 27
Amensalism, model of mixed culture interaction, 538–539
Amino acids. See also Proteins.
in cell construction. See Cell construction, amino acids.
chemical structure, 31
a dipolar molecule, 32
isoelectric point, 32
natural, 31
peptide bond, 32
in polypeptides, 31
proteinogenic, 31
pyrrolysine, 31
selenosysteine, 31
zwitterion, 32
Aminoacyl site, 125
Aminoacyl-tRNA synthetases, 125
Amoebae, 27
AMP (adenosine monophosphate), 45
Amplifying DNA, 260. See also PCR (polymerase chain reaction).
Amylases, 101
Amylopectin, 41
Amylose, 41
Anabolism, definition, 146
Anaerobic bioprocesses. See also Aerobic bioprocesses.
lactic acid production, 581–584
Anaerobic digestion, biological waste treatment, 564–566
Anaerobic metabolism
anaerobic respiration, 161
denitrification, 161
ED (Entner–Doudoroff) pathway, 161
fermentation, 161
Anaerobic organisms, 14
Anaerobic respiration, 149, 161
Anchorage-dependent cells, 432, 435
Animal cell cultivation
anchorage-dependent cells, 435
cancer linkage to cell transformation, 435
contact inhibition, 435
continuous cells, 435
hybridoma cells, 436
immortal cells, 435
mammalian cell culture, 436–437
mortal cells, 435
nonanchorage-dependent cells, 435
secondary culture, 435
senescence, 435
Animal cell cultivation, bioreactor considerations
constraints, 443
entrapped cells in stirred reactors, 445–447
hollow-fiber reactors, 445
nonstirred reactor systems, 444–445
single-use disposable systems, 445, 447
stirred-tank bioreactors, 447
suspended cultures, 447
Animal cells
actin filaments, 433
anchorage-dependent cells, 432
centrosome, 433
cilia, 433
cisternae, 433
cytoskeleton, 433
cytosol phase cytoplasm, 432
dictyosome, 433
ER (endoplasmic reticulum), 432
glyoxysomes, 433
Golgi body, 433
intermediate filaments, 433
lumenal phase cytoplasm, 432
lysosomes, 432
metabolism of nutrients, 433–434
microtubules, 433
microvilli, 432
mitochondria, 432
nucleoli, 433
perinuclear space, 433
peroxisomes, 433
size, 431
types of filaments, 433
Animal vs. plant eucaryotes, 22
Anisotropic membranes, separation of soluble products, 395
Anoxygenic photosynthetic bacteria
bacteriochlorophyll, 19
light-gathering pigments, 19
in photosynthesis, 19
Antibodies, proteins. See Proteins, antibodies.
Antibody (Ab) macromodule, 34
Antibody–antigen complex, 36
Antibody–antigen interaction, 36
Antibody–drug conjugate (ADC), 36
Anticancer agent (Taxol), in plant cell cultivation, 456–457
Anticodons, 125
Antigen (Ag) macromodule, 34, 36
Apoenzyme, 61
Apparent growth yield, 179–180
Aqueous two-phase affinity partition extraction, separation of soluble products, 389
Aqueous two-phase extraction, separation of soluble products, 389–390
procaryotes, 15
structure of, 20
Artificial tissue/organs, 520–521
Ascospores, 25
Asexual reproduction
eucaryotes, 23
microscopic eucaryotes, 25
Asparaginase, uses for, 102
maintenance coefficient, 227–229
phosphate bonds, 45
regularities, 229
ATP (adenosine triphosphate), yield coefficients
theoretical predictions, 235–236
Autographa californica (baculovirus), 265, 480
Autologous implantation, 523
Autotrophic metabolism, 163–165
Autotrophs, 52
B
description, 19
genetic engineering, host-vector systems, 477
Bacillus (cylindrical) cells, 14
Bacillus (rod) cells, 14
Bacteria. See also Archaebacteria; Eubacteria (true bacteria).
architecture of, 21
capsule, 20
chromatophores, 20
endospores, 20
Gram staining, 18
intracellular spores, 20
outside cell wall. See Capsule.
photosynthesis, 20
Bacterial microcompartments (BMCs), 20
Bacteriochlorophyll, 19
Bacteriophages. See Phages.
Baculovirus (Autographa californica), 265, 480
Baker’s yeast production, 588–590
Balanced growth, 177
Balanced growth assumption, 192
Bardenpho process, biological waste treatment, 571
Basal level of proteins, 131
Basic local alignment search tool (BLAST), 271
genetic instability, 277
market economics, 277
operability, 277
semicontinuous. See Fed-batch bioreactors.
variable-volume continuous culture. See Fed-batch bioreactors.
chemostat with recycle, 278–281
external membrane bioreactors, 295
internal membrane bioreactors, 295
multistage chemostat systems, 281–287
Batch cell growth, growth patterns
apparent growth yield, 179–180
balanced growth, 177
death phase, 179
deceleration phase, 178
decline phase, 179
diauxic growth, 177
endogenous metabolism, 178
exponential phase, 177
growth-associated products, 183
Luedeking–Piret equation, 183
maintenance, 180
maintenance energy, 178
microbial products, classifying, 183–184
mixed-growth-associated product formation, 183
nongrowth-associated product formation, 183
nongrowth-related functions, 181–182
phases, 175
primary metabolites, 178
secondary metabolites, 178
yield factors for aerobic growth, 182
Batch cell growth, quantifying
cell concentration, quantifying, 170
cell mass concentration, determining, 171–175
cell number density, determining, 171
counting viable cells, 171
direct cell counting, 171
direct methods, 172
dry weight, determining, 171–172
hemocytometer, 171
optical density, 172
packed cell volume, 172
particle counters, 171
Petroff–Hausser counting chamber, 171
plate counts, 171
turbidity, 172
viable count, 171
critical oxygen concentration, 187–188
DO (dissolved oxygen) effects, 187–188
environmental conditions, effects of, 184–189
heat generated by microbial growth, 190–191
OTR (oxygen transfer rate), 188
OUR (oxygen uptake rate), 188
pH effects, 186
redox potential, 189
Batch cell growth kinetics, quantifying
balanced growth assumption, 192
Blackman equation, 194
cell structure, 191
chemically structured models, 202–207
Contois equation, 194
extrinsic concentration, 202
half-velocity constant, 192–193
intrinsic concentration, 202
maximum growth potential, 200–201
models for filamentous organisms (molds), 201
models for transient behavior, 201–202
models with growth inhibitors, 195–197
models with time delays, 202
Moser equation, 194
product inhibition, 196
segregation, 191
structured models, 191
substrate inhibition, 195
substrate-limited growth, 192–194
Tessier equation, 194
unbalanced growth, 191
unstructured nonsegregated models, 192–201
Bed depth–service time equation, separation of soluble products, 405–409
Bidirectional DNA, 117
Binding, immobilized cell systems, 300–302
vs. bioprocess engineering, 3
bioreaction engineering, 2
bioseparations, 2
definition, 2
Biochemistry of animal cells, 431–434
Biodegradation of xenobiotics (toxic aromatic compounds), 157–158
Bioelectricity from wastes, 598–600
Bioengineering, definition, 2
Bioengineers, definition, 2
Biofuel and bioenergy production
bioelectricity from wastes, 598–600
gaseous fuels from biomass, 597–598
hydrogen gas production, 597–598
liquid fuel production, 596–597
MFCs (microbial fuel cells), 598–600
Bioinformatics, 271
Biological engineering, definition, 2
Biological oxygen demand (BOD), 550
Biological waste treatment. See Mixed culture, biological waste treatment.
Biologists
research approaches, 3
Biomedical engineering, definition, 2
Biomolecular engineering, definition, 2
Biopharmaceutical products from genetic engineering, 473
vs. biochemical engineering, 3
industrial uses for. See Aerobic bioprocesses; Anaerobic bioprocesses; Biofuel and bioenergy production.
origins of, 8
Bioprocess engineering, medical uses for
artificial tissue/organs, 520–521
autologous implantation, 523
bioreactor considerations. See Bioreactors, bioprocess engineering.
cartilage replacement, 522–523
endocytosis, 525
endosomes, 525
gene therapy using viral vectors, 523–528
mass production of retrovirus, 527–528
models of viral infection, 524–527
regenerative medicine, 519–523
viral gene delivery systems, 524
Bioprocesses, regulatory constraints, 9–10
Bioreaction engineering, 2
Bioreactor considerations, animal cell cultivation
constraints, 443
entrapped cells in stirred reactors, 445–447
hollow-fiber reactors, 445
nonstirred reactor systems, 444–445
single-use disposable systems, 445, 447
stirred-tank bioreactors, 447
suspended cultures, 447
Bioreactor considerations, plant cell cultivation
ajmalicine from periwinkle, 465
mixotrophic cultures, 467
photoperiod control, 467
root mats, 467
submerged culture, 467
Bioreactor instrumentation and control
of chemical environment, 350–351
control strategies, 355
data logging, 354
exit-gas measurement, 352
FTIR (Fourier transform infrared), 352
gateway sensors, 354
HPLC (high-pressure liquid chromatography), 352
measuring active fermentation, 349–352
of physical environment, 350
probe drift, 351
probe fouling, 351
recalibrating probes in situ, 351
using information from, 352–355
Bioreactor scale-up
bioreactors, definition, 324
fermenters, definition, 324
geometric similarity, 337
internal mechanical agitation, 324–329
overview of reactor types, 324
practical limits, 341
Rushton impeller, 325
Bioreactor scale-up, common difficulties
bubble column reactors, 329–330
cleaning, 329
dynamic method for oxygen removal, 335
energy efficiency, 329
foaming, 328
internal mechanical agitation, 324–329
single-use bioreactors, 330–331
steady-state method for oxygen removal, 334
sterility, 329
unsteady-state method for oxygen removal, 333
working volume, 328
Bioreactors. See also Batch bioreactors; Continuous bioreactors.
cleaning, 329. See also Sterilizing process fluids.
cultivation method, choosing, 276–278
definition, 324
immobilized cell systems, 309–311
mixed and forcefully aerated, 314
overview of reactor types, 324
packed-bed, 314
rotating drum, 314
for solid-state fermentation, 313–316
spargers, 324
sterilizing. See Sterilizing process fluids.
tray, 314
Bioreactors, medical applications
body-on-a-chip systems, 530–531
extracorporeal artificial liver, 530
flatbed reactors, 530
fluidized bed reactors, 530
iPS (induced pluripotent stem) cells, 529
membrane-based units, 530
microphysiological systems, 531
multiorgan-on-a-chip systems, 531
PBPK (physiologically based pharmacokinetic) model of the human body, 531
pluripotent stem cells, 529
progenitor cells, 529
Bioseparations, 2
gluconeogenesis, 160
HMP (hexose monophosphate) pathway, 158–161
Biotechnology, definition, 2
Blackman equation, 194
BLAST (basic local alignment search tool), 271
Blue-green algae (cyanobacteria)
growth environment, 14
photosynthesis, 19
BMCs (bacterial microcompartments), 20
BOD (biological oxygen demand), 550
Body-on-a-chip systems, 530–531
Bottle plant, penicillin production, 6
Briggs, G. E., 66
Bubble column reactors, scaling up, 329–330
C
Cabbage looper (Tricoplusia ni), 480
Cake resistance, separation of insoluble products, 376–378
Callus cultures in plant cell cultivation, 458–459
Campylobacter jejuni bacterium, 129
Cancer
bioprocesses for the anticancer agent Taxol, 456–457
linkage to cell transformation, 435
transformed cells, 479
Capsid coating, viruses, 17
Capsule, bacteria, 20
Carbohydrates
amylopectin, 41
amylose, 41
cellulose, 41
deoxyribose, 39
disaccharides, 40
D-ribose, 39
glycans, 42
glycogen, 41
glycosylation, 42
lactose, 40
photosynthesis, 37
role in cells, 37
sucrose, 40
Carbon compounds, macronutrients, 52–53
Cartilage replacement, 522–523
definition, 146
Catabolite repression, 131
Catalytic proteins, 30
cDNA (complementary DNA), 260
CDRs (complementarity determining regions), 36
Cell concentration, quantifying, 170
Cell construction
composition of living cells, 28
integral member proteins, 43
nucleic acids, 44–51. See also DNA (deoxyribonucleic acid); RNA (ribonucleic acid).
peripheral member proteins, 43
PHA (polyhydroxyalkanoates), 44
PHB (polyhydroxybutyrate), 44
phosphoglycerides, 43
phospholipids, 43
scientific domain. See Systems biology.
Cell construction, amino acids. See also Proteins.
chemical structure, 31
a dipolar molecule, 32
isoelectric point, 32
peptide bond, 32
in polypeptides, 31
proteinogenic, 31
pyrrolysine, 31
selenosysteine, 31
zwitterion, 32
batch cell growth, 179
and thermodynamic equilibrium, 51
Cell disruption, separation of insoluble products
Cell division among eucaryotes, 23, 26
culturing cells in a vessel. See Batch cell growth.
growth factors, 139
net specific growth rate, 169–170
rate of microbial growth, 169–170
Cell growth in continuous culture
overview, 208
PFRs (plug flow reactors), 208, 210
Cell growth in continuous culture, chemostats
CFSTR (continuous-flow, stirred-tank reactor), 210
deviations from ideality, 218
maintenance coefficient, 213
mutations, 217
washing out a culture, 211
Cell lysis, 18
Cell mass concentration, determining, 171–175
Cell motion, eucaryotes, 24–25
archaebacteria, 15
by cell structure, 15. See also Eucaryotes; Procaryotes.
definition, 15
dual names, 15
eubacteria (true bacteria), 15
genes of a whole organism. See Genome.
genus, 15
Latin names, 15
for microorganisms, 15
for organizing knowledge. See Cell taxonomy.
within procaryotes, 15
recognized subdivisions of organisms, 16
viruses, 15
Cell number density, determining, 171
categories of, 51. See also Macronutrients; Micronutrients.
intracellular composition of cells, 51–52
thermodynamic equilibrium and death, 51
Cell receptors, role of, 137–139
Cell separation. See Separation.
Cell shapes
cylindrical (bacillus), 14
rod (bacillus), 14
spherical, elliptical (coccus), 14
spiral (spirillum), 14
for naming organisms. See Cell nomenclature.
for organizing knowledge, 14–15
Cell-free protein synthesis (CFPS), 484
Cells. See also DNA (deoxyribonucleic acid); RNA (ribonucleic acid).
acylation, 115
aerotaxis, 138
alkylation, 116
cell receptors, role of, 137–139
cellular differentiation, 137–139
chemotaxis, 138
codons. See Genetic code.
cotranslational modifications, 115–116
disulfide bond formation, 115
energy-independent uptake, 135–137
estimation of elemental composition, 236–237
facilitated diffusion, 135–137
genes, 116–117. See also Genetic code.
genetic code. See Genetic code.
glycosylation, 115
hormones, 139
hydroxylation, 116
inteins, 116
introns, 116
lipidation, 116
macromolecules. See DNA (deoxyribonucleic acid); Protein; RNA (ribonucleic acid).
major groups of. See Eucaryotic cells; Procaryotes.
metabolic regulation. See Metabolic regulation.
mRNA splicing, 116
with or without oxygen. See Facultative organisms.
oxygen toxicity. See Anaerobic organisms.
phosphorylation, 116
phosphotransferase system, 137
phototaxis, 138
posttranslational modification, 115–116
protein splicing, 116
replication, 114
retrotransposons, 115
reverse transcriptase, 115
reverse transcription, 115
sensing external environment, 135–139
steroid hormone receptors, 139
sulfation, 116
telomere synthesis, 115
transcription to RNA. See DNA transcription.
transfer of biological information, 114–117
translation into proteins, 114, 127–129
transporting small molecules across membranes, 135–137
ubiquitination, 116
ubiquitins, 116
using oxygen. See Aerobic organisms.
Cells and their environments
acidophiles, 14
aerobic organisms, 14
alkaliphiles, 14
anaerobic organisms, 14
cyanobacteria, 14
extreme. See Extremophiles.
facultative organisms, 14
high salt concentrations. See Halophiles.
high temperatures. See Thermophiles.
low temperatures. See Psychrophiles.
mesophiles, 14
with minimal nutrients. See Cyanobacteria.
moderate temperatures. See Mesophiles.
neutrophiles, 14
oxygen adaptive. See Facultative organisms.
oxygen inhibited. See Anaerobic organisms.
oxygen required. See Aerobic organisms.
pH values 1 or 2. See Acidophiles.
pH values 6 to 8. See Neutrophiles.
pH values above 9. See Alkaliphiles.
psychrophiles, 14
thermoacidophiles, 21
thermophiles, 14
Cell-surface display, 265
Cellular differentiation, 137–139
Cellulases, 101
Cellulose, 41
Centrifugal Podbielniak extractors, separation of soluble products, 387–388
Centrifugation, separation of insoluble products, 378–382
Centrifugation coefficient, separation of insoluble products, 381
Centrosome, 433
Cer locus, 493
CFPS (cell-free protein synthesis), 484
CFSTR (continuous-flow, stirred-tank reactor), 210, 552
Chain, Ernst, 4
Chaperones, 125
Chelating agents, 55
Chemautotrophs, 52
Chemical agents for causing mutations, 250
Chemical environment, monitoring, 350–351
Chemical gene synthesis, 259
Chemical oxygen demand (COD), biological waste treatment, 550
Chemical synthesis, penicillin production, 5
Chemical waste treatment, 549
Chemically structured models, 202–207
Chemostat with recycle bioreactor, 278–281
Chemostats
CFSTR (continuous-flow, stirred-tank reactor), 210
deviations from ideality, 218
maintenance coefficient, 213
mutations, 217
washing out a culture, 211
Chemotaxis, 138
Chlorella algae, 27
Chloroplast, 165
Chloroplasts, 24
CHO (Chinese hamster ovary) cells, 479–480, 484–485
Chromatography. See Separation of soluble products, chromatography.
Chromatophores, 20
Chromosomes, 22
Ciliated organisms
definition, 25
vs. flagellated organisms, 25
CIP (clean-in-place) technology, 329
Cisternae, 433
Citric acid cycle, 149
Citric acid production, 586–588
Cleaning bioreactors, 329. See also Sterilizing process fluids.
Cloning
alternative strategies, 262–263
amplifying DNA, 260
cDNA (complementary DNA), 260
cell-surface display, 265
chemical gene synthesis, 259
codon harmonization, 259
codon optimization, 259
DNA microarray technology, 259
expressed DNA, 262
expression of cloned genes, 263–265
Gateway cloning, 262
Gibson assembly, 262
Golden Gate cloning, 263
GreenGate cloning, 263
hybridization, 259
immunoblot testing, 264
inserting genes into DNA, 260–262
introns, 259
isothermal cloning, 262
LIC (ligation independent cloning), 263
ligands, 265
MoClo (molecular cloning), 263
obtaining the gene of interest, 259–260
overview, 258
PCR (polymerase chain reaction), 260
phage display, 265
plasmid vectors, 260
probes, 259
recombinant DNA techniques, 258
restriction endonuclease, 262–263
reverse transcriptase, 260
synonymous mutations, 259
TA cloning, 262
testing for proteins, 264
TOPO cloning, 262
Western blot testing, 264
yeast-mediated cloning, 263
Clustered regularly interspaced short palindromic repeat (CRISPR), 267, 480
Coagulation, separation of insoluble products, 382
Coccus (elliptical) cells, 14
Coccus (spherical) cells, 14
COD (chemical oxygen demand), biological waste treatment, 550
Coding DNA, 49
Coding RNA, 48
Codon harmonization, 259
Codon optimization, 259
Commensalism, model of mixed culture interaction, 538
Commonly added micronutrients, 54
Competent DNA strains, 254
Competition, 536
Competitive inhibitors, enzyme kinetics, 73–74
Complementarity determining regions (CDRs), 36
Complementary DNA (cDNA), 260
Complex glycoforms, 129
Concentration, separation of soluble products, 403
Concentration polarization, separation of soluble products, 394–395
Concerted feedback inhibition, 134
Conditional mutants, 251
Conidia, 25
Constitutive exocytosis pathway, 127
Constitutive genes, 132
Contact inhibition, 435
Contact stabilization, biological waste treatment, 557
CFSTR (continuous-flow, stirred-tank reactor), 276–278
Continuous bioreactors, modifying
chemostat with recycle, 278–281
external membrane bioreactors, 295
internal membrane bioreactors, 295
multistage chemostat systems, 281–287
Continuous sterilization, 361
Continuous-flow, stirred-tank reactor (CFSTR), 210, 552
Contois equation, 194
Control sites in aerobic glucose metabolism, 154–155
Cooperative feedback inhibition, 134
Core enzymes, 119
Cost of sequencing a complete genome, 270
Cotranslational modifications, 115–116
Cotranslational protein translation, 125
Counting viable cells, 171
CRISPR (clustered regularly interspaced short palindromic repeat), 267, 480
Cristae, 23
Cross-flow filtration, separation of soluble products, 398–403
Cross-flow ultrafiltration, separation of soluble products, 398–403
Crystallization, purification process, 422–423
Cumulative feedback inhibition, 134
Cyanobacteria (blue-green algae)
growth environment, 14
photosynthesis, 19
Cylindrical (bacillus) cells, 14
Cytokinesis, 23
Cytoskeleton
animal cells, 433
eucaryotic cells, 25
Cytosol phase cytoplasm, 432
D
Dalton, 36
Damkohler number, 91
Dark phase of photosynthesis, 164
Data logging, 354
Death. See Cell death.
Deceleration phase, 178
Decline phase, 179
Degenerate code, 123
Deletion mutations, 248
Denatured enzymes, 71
Denitrification, 161
Deoxyribonucleic acid (DNA). See DNA (deoxyribonucleic acid).
Deoxyribonucleotides, structure of, 46
Deoxyribose, 39
Diafiltration, separation of soluble products, 403
Dialysis, separation of soluble products, 392–393
Dialysis equilibrium, separation of soluble products, 393
Dictyosome, 433
Differentiated tissue in plant cell cultivation, 459
Dimers, 487
Diploid cells, 23
Direct cell counting, 171
Direct methods for counting viable cells, 172
Direct selection mutation, 250
Directed evolution, 512
Disaccharides, 40
Disinfection vs. sterilization, 356
Displacement chromatography, 409
Disposable bioreactors. See Single-use bioreactors.
Dissociation extraction, separation of soluble products, 387–388
Dissolved oxygen (DO) effects in batch cell growth kinetics, 187–188
Disulfide bond formation, 115
DNA (deoxyribonucleic acid). See also Cells; Nucleic acids; RNA (ribonucleic acid).
amplifying, 260. See also PCR (polymerase chain reaction).
building blocks of. See Nucleotides.
coding sequences, 49
competent strains, 254
DNA methylases, 116
donor, 253
double helix, 48
forming RNA molecules. See DNA transcription.
junk DNA. See Noncoding DNA.
major functions of, 48
methylation variation, 116
noncoding DNA, 49
plasmids, 48
proofreading, 118
structure of, 47
Taq (Thermus aquaticus), 14
DNA gyrase enzyme, 117
DNA ligase enzyme, 118
DNA microarray technology, 259
semiconservative replication, 48–49, 117
DNA replication in E. coli. See also E. coli.
bidirectional DNA, 117
DNA gyrase enzyme, 117
DNA ligase enzyme, 118
lagging strands, 118
leading strands, 118
Okazaki fragments, 118
origin of replication, 117
proofreading the DNA, 118
replication forks, 117
unwinding enzymes, 117
core enzymes, 119
definition, 48
holoenzymes, 119
mRNA, 121
mRNA splicing, 122
nonsense DNA, 122
polyadenylation, 122
polygenic messages, 121
primary products of, 119
procaryotic vs. eucaryotic cells, 121–122
promoter region, 121
reading through a terminator, 121
reverse transcription, 115
rho protein, 121
RNA polymerase enzyme, 119
rRNA, 121
separate protein for each gene, 121
sigma factor, 119
stable RNA species, 121
stop signals, 121
strong promoter, 121
strong terminators, 121
transcription terminators, 121
tRNA, 121
unstable RNA species, 121
weak terminators, 121
aminoacyl site, 125
aminoacyl-tRNA synthetases, 125
anticodons, 125
chaperones, 125
cotranslational protein translation, 125
initiation complex, 125
initiation factors, 125
nonsense codons, 125
peptides from RNA, 48
peptidyl site, 125
posttranslation movement across membranes, 125
posttranslational processing, 125–129. See also Eucaryotic cells, posttranslational protein release; Procaryotic cells, posttranslational protein release.
proteins from RNA, 48
RF (release factor), 125
signal peptides, 125
stop codons, 125
DO (dissolved oxygen) effects in batch cell growth kinetics, 187–188
Domestic wastes, biological waste treatment, 549
Donnan equilibrium, separation of soluble products, 393
Donor DNA, 253
Double helix, 48
Double-reciprocal plot, 68
D-ribose, 39
Dry weight of cells, determining, 171–172
Drying, purification process, 423–424
Dunaliella algae, 27
Dynamic method for oxygen removal, 335
Dyno-Mill homogenizer, separation of insoluble products, 384
E
cell lysis, 18
cells breaking open. See Cell lysis.
conversion of aspartic acid to aspartyl phosphate, 140–142
cytoplasmic membrane, 18
description, 18
DNA replication. See DNA replication in E. coli.
genetic engineering, host-vector systems, 475–477, 484–485
inner membrane, 18
LPS (Lipopolysaccharide), 18
LPS removal, 18
outer membrane, 18
peptidoglycan, 18
periplasmic space, 18
strong promoters, 491
ED (electrodialysis), separation of soluble products, 421–422
ED (Entner–Doudoroff) pathway, 161
Effectiveness factor, enzyme immobilization, 95–96
Egg cells, 23
Elder, A. L., 5
Electron transport chain, 149, 152–154
Electrophoresis
expression of cloned genes, 263–264
separation of soluble products, 419–420
two-dimensional gel electrophoresis, 270
Electroporation, 265
Electrostatic effects on enzyme immobilization, 98
Elicitors in plant cell cultivation, 460–461
Elliptical (coccus) cells, 14
Elution chromatography, 409
EMP (Embden–Meyerhof–Parnas) pathway, 149–152
Encapsulation, cell entrapment, 300
Endocytosis, 525
Endogenous metabolism, 178
Endoplasmic reticulum (ER), 23–24, 432
Endosomes, 525
Endospores, 20
Endotoxins. See LPS (Lipopolysaccharide).
End-product inhibition, 133
Energy efficiency, bioreactors, 329
Energy-independent uptake, 135–137
Engineered antibodies, 36
Engineers
research approaches, 3
Enhancer regions, 131
Entner–Doudoroff (ED) pathway, 161
Entrapment, active cell immobilization, 298–300, 302
Entrapped cells in stirred reactors, 445–447
Environmental conditions, batch cell growth kinetics, 184–189
Enzyme activation, 80
Enzyme immobilization
electrostatic effects, 98
steric effects, 98
Enzyme immobilization, diffusional limitations
Damkohler number, 91
on enzymes immobilized in a porous matrix, 93–97
on reaction rate, 93
on surface-bound enzymes, 91–93
Enzyme immobilization, methods of
adsorption, 87
diffusion limitations, 87
enzyme leakage, 87
microencapsulation, 87
Enzyme induction, 131
Enzyme kinetics. See also Michaelis–Menten kinetics.
enzyme activation, 80
Langmuir–Hinshelwood kinetics, 63
multiphase enzymatic reactions, 84–85
partition coefficient, 85
RST (rate of substrate transfer), 85
saturation kinetics, 63–65. See also Michaelis–Menten kinetics.
temperature inactivation, 83
thermal denaturation, 83
Enzyme kinetics, inhibited
inhibitors, 73
irreversible inhibitors, 73
mixed inhibition, 76
noncompetitive inhibitors, 73, 74–75
reversible inhibitors, 73
uncompetitive inhibitors, 75–76
Enzyme kinetics, mechanistic models
quasi-steady-state assumption, 66–67
rapid-equilibrium assumption, 65–66
Enzyme leakage, 87
Enzymes. See also specific enzymes.
apoenzyme, 61
classification, 62
containing protein groups, 61
denatured, 71
enzyme-substrate interaction, 63
holoenzymes, 61
induced fit model, 63
integral membrane proteins, 30
isozymes, 61
lock-and-key model, 63
naming, 61
orientation effect, 63
proximity effect, 63
regulatory, 30
structure of, 61
units, 70
Enzyme-substrate interaction, 63
Episomes, gene transfer and rearrangement, 256–257
Epitopes, 36
ER (endoplasmic reticulum), 432
Eroshin, V. K., 229
Error-prone PCR, 512
evolution of, 15
Gram staining, 18
photosynthesis, 19
Eucaryotes. See also Procaryotes.
actin filaments, 25
animal vs. plant, 22
asexual reproduction, 23
chloroplasts, 24
chromosomes, 22
cilia, 25
ciliates, 25
cristae, 23
cytokinesis, 23
cytoplasmic membrane, 22
cytoskeleton, 25
diploid cells, 23
egg and sperm cells, 23
gametes, 23
glycans, 24
glycosylation, 24
glyoxysomes, 24
Golgi bodies, 24
haploid cells, 23
histones, 22
inner membranes, 23
intermediate filaments, 25
interphase, 23
lysosomes, 24
microtubule, 25
mitosis, 23
nucleus, 22
peroxisomes, 24
photosynthesis, 24
vs. procaryotes, 22
sexual reproduction, 23
size, 22
sterols, 22
thylakoids, 24
tubulin, 25
vacuoles, 24
zygotes, 23
algae, 27
ascospores, 25
asexual reproduction, 25
fission reproduction, 25
fungi, 25
yeasts, 25
in genetic engineering, host-vector systems, 477–479
vs. procaryotic cells, DNA transcription, 121–122
Eucaryotic cells, posttranslational protein release
Campylobacter jejuni bacterium, 129
complex glycoforms, 129
constitutive exocytosis pathway, 127
exocytosis, 127
glycans, 127
glycosylation, 127
Golgi apparatus, 127
Golgi trans face, 127
hybrid glycoforms, 129
N-linked glycosylation, 129
OST (oligosaccharyltransferase), 129
protein release, 127
PTMs (posttranslational modifications), 127
regulated exocytosis pathway, 127
simple glycoforms, 129
transport vesicle fusion, 127
Exit-gas measurement, 352
Exocytosis, 127
Exponential growth phase, 177
Expressed DNA, 262
Expression of cloned genes, 263–265
External membrane bioreactors, 295
Extracorporeal artificial liver, 530
Extremophiles, 13–14, 21. See also Archaebacteria.
Extrinsic concentration, 202
F
Facilitated diffusion, 135–137
Facultative autotrophs, 52
Facultative organisms, 14
Fall armyworm (Spodoptera frugiperda), 480
Fats in cell construction, 42–45
Fatty acids
definition, 42
examples, 42
fats, 42
FDA (Food and Drug Administration), 10–11
Fed-batch bioreactors, 288–293
Fermentation
definition, 161
glycolysis, 149
molds, 27
two-phase, 489
Fermenter, 324. See also Bioreactor.
Fibrous proteins, 30
Filter sterilization, 361
Filtration, separation of soluble products
cross-flow filtration, 398–403
cross-flow ultrafiltration, 398–403
diafiltration, 403
MF (microporous filtration), 395–398
rejection coefficient of an ultrafilter, 399–400
tangential flow filtration, 398–403
UF (ultrafiltration), 395–398, 403
Fission reproduction, microscopic eucaryotes, 25
Fixed solids, biological waste treatment, 551
Flagellate motion, 27
Flagellated organisms vs. ciliated organisms, 25
Flagellates, 27
Flat sheet membranes, separation of soluble products, 400–402
Flatbed reactors, 530
Flocculation, separation of insoluble products, 382
Florey, Howard, 4
Fluidized bed reactors, 530
Fluorescence, 165
Foaming, bioreactor scale-up, 328
Food and Drug Administration (FDA), 10–11
Fourier transform infrared (FTIR), 352
Freeze drying, purification process, 423
French presses, separation of insoluble products, 383
Freundlich adsorption isotherm, separation of soluble products, 403–404
Friable calli in plant cell cultivation, 459
Frontal chromatography, 409
FTIR (Fourier transform infrared), 352
Full inhibition, 134
Fumarate, converting to L-aspartate, 102
Functional genomics, 267
Fungi
ascomycetes, 27
basidiomycetes, 27
definition, 25
deuteromycetes, 27
genetic engineering, host-vector systems, 478
modes of sexual reproduction, 27
phycomycetes, 27
G
Gametes, 23
Gaseous fuels from biomass, 597–598
Gateway cloning, 262
Gateway sensors, 354
Gaulin–Manton presses, separation of insoluble products, 383
Gelation of polymers, 299
Gel-filtration chromatography, 410–411, 414–415
Gene libraries, generating, 512–513
Gene therapy using viral vectors, 523–528
Gene transfer and rearrangement. See also Mutations.
competent strains, 254
donor DNA, 253
generalized transduction, 254–255
genetic recombination, 252–254
internal gene transfer, 257
lysogenic cells, 255
main mechanisms, 252. See also specific mechanisms.
plasmid vectors, 254
prophage conversion, 256
restriction endonucleases, 253
specialized transduction, 255
temperate phages, 256
transformation, 254
transposons, 257
Generalized transduction, gene transfer and rearrangement, 254–255
anticodons, 125
degenerate code, 123
Genetic engineering. See also Mutations.
baculovirus, 265
biopharmaceutical products, 473
cer locus, 493
directed evolution, 512
electroporation, 265
error-prone PCR, 512
generating gene libraries, 512–513
metabolic control theory, 510
metabolic engineering, 506–509
metabolic flux analysis, 510
origins of replication, 490
overview, 258
par locus, 493
plasmid design problems, 490–493
protein products vs. nonprotein products, 472–474
protoplast fusion, 265
protoplasts, 265
random mutagenesis, 512
rational design, 512
regulatory constraints on, 503–506
runaway replication, 490
semirational design, 513
site-directed mutagenesis, 512
Genetic engineering, basic elements
alternative cloning strategies, 262–263
amplifying DNA, 260
cDNA (complementary DNA), 260
cell-surface display, 265
chemical gene synthesis, 259
codon harmonization, 259
codon optimization, 259
DNA microarray technology, 259
expressed DNA, 262
expression of cloned genes, 263–265
Gateway cloning, 262
Gibson assembly, 262
Golden Gate cloning, 263
GreenGate cloning, 263
hybridization, 259
immunoblot testing, 264
inserting genes into DNA, 260–262
introns, 259
isothermal cloning, 262
LIC (ligation independent cloning), 263
ligands, 265
MoClo (molecular cloning), 263
obtaining the gene of interest, 259–260
overview, 258
PCR (polymerase chain reaction), 260
phage display, 265
plasmid vectors, 260
probes, 259
recombinant DNA techniques, 258
restriction endonuclease, 262–263
reverse transcriptase, 260
synonymous mutations, 259
TA cloning, 262
testing for proteins, 264
TOPO cloning, 262
Western blot testing, 264
yeast-mediated cloning, 263
Genetic engineering, genetic instability
dimers, 487
growth-rate-dominated instability, 489–490
high-copy-number plasmids, 486
host-vector interactions, 493–503
low-copy-number plasmids, 486
metabolic burden, 489
multimers, 487
overview, 486
plasmid structural instability, 488
selective pressure, 489
tetramers, 487
two-phase fermentation, 489
Genetic engineering, host-vector systems, 474
A. nidulans, 478
B. subtilis, 477
baculovirus (Autographa californica), 480
cabbage looper (Trichoplusia ni), 480
CFPS (cell-free protein synthesis), 484
CHO (Chinese hamster ovary) cells, 479–480, 484–485
comparison of strategies, 484–485
continuous cells, 479
CRISPR (clustered regularly interspaced short palindromic repeat), 480
fall armyworm (Spodoptera frugiperda), 480
fungi, 478
gram-positive bacteria, 476
H. polymorpha, 478
heat shock, 475
identification of pathway enzymes, 508–509
immortal cells, 479
inclusion bodies, 475
insect cell–baculovirus system, 480–482
L. lactis, 477
lower eucaryotic cells, 477–479
native hosts, 508
NOVs (nonoccluded viruses), 481
P. pastoris, 478
protein secretion/excretion, 476
signal peptides, 476
Streptomyces, 477
transformed cells, 479
transgenic plants and plant cell culture, 483–484
yeasts, 478
Genetic instability. See Genetic engineering, genetic instability.
Genetic recombination, gene transfer and rearrangement, 252–254
Genetic-level control, 130–133
Genome engineering. See also Genetic engineering; Genomics.
CRISPR (clustered regularly interspaced short palindromic repeat), 267
customizing meganucleases, 266–267
eliminating genes, 266
introducing targeted modifications into chromosomes, 266
MAGE (multiplex automated genome engineering), 266
molecular scissors, 266
Genomes
editing. See Genome engineering; Genomics.
Genomics. See also Genome engineering.
bioinformatics, 271
BLAST (basic local alignment search tool), 271
computational techniques, 271
definition, 267
functional, 267
homologous amino acid sequences, 271
ORFs (open reading frames), 271
overview, 267
proteomics, 267
systems biology, 267
Genomics, experimental techniques
cost of sequencing a complete genome, 270
high-throughput sequencing, 269
Illumina sequencing, 269
isoelectric points, 270
microarrays, 270
nanopores, 269
NGS (next-generation sequencing), 269
SBS (sequencing by synthesis) sequencing, 269
transcriptomics, 270
two-dimensional gel electrophoresis, 270
Genotype, definition, 248
Genus, 15
Gibson assembly, 262
Glass wool filters, 362
Globular proteins, 30
GLP (good laboratory practices), 10
Glucanases, 102
Gluconeogenesis, 160
Glucose
converting to fructose, 102
Glucose effect, 131
Glycogen, 41
aerobic respiration, 149
anaerobic respiration, 149
citric acid cycle, 149
electron transport chain, 149, 152–154
fermentation, 149
phases, 149
respiration, 149
TCA (Krebs, tricarboxylic acid), 149
Glycosylation, 24, 42, 115, 127
GMP (good manufacturing process), 10
Golden Gate cloning, 263
Golgi apparatus, 127
Golgi trans face, 127
Good laboratory practices (GLP), 10
Gram, Hans Christian, 18
bacteria, 18
colorless reaction, 18
eubacteria (true bacteria), 18
negative reaction, 18. See also E. coli.
no reaction, 19
positive reaction, 18. See also B. subtilis.
procaryotes, 20
purple reaction, 18
red reaction, 18
Gram-positive bacteria, 476
GreenGate cloning, 263
Growing cells. See Cell growth.
Growth dynamics of animal cells, 441–443
Growth media, animal cell cultivation, 437–441
Growth-associated products, 183
Growth-rate-dominated instability, 489–490
Grow-through tests, 363
GTP (quanosine triphosphate), 45
H
H. polymorpha, 478
Hairy roots, bioreactor considerations in plant cell cultivation, 466–467
Haldane, J. B. S., 66
Half-velocity constant, 192–193
Haploid cells, 23
HC (hydrophobic chromatography), 411
Heat generated by microbial growth, 190–191
Heat shock, 475
Heatley, Norman, 4
Helical structures in proteins, 33–34
Hemicellulases, 102
Hemocytometer, 171
Henri, V. C. R., 63
Heterotrophs, 52
HFCS (high-fructose corn syrup) production, 593–595
HIC (hydrophobic interaction chromatography), 411
High-copy-number plasmids, 486
High-pressure liquid chromatography (HPLC), 352, 411
High-throughput sequencing, 269
Hindered settling, separation of insoluble products, 378–380
Histones, 22
HIV (human immunodeficiency) virus, reverse transcription, 115
HMP (hexose monophosphate) pathway, 158–161
H/O (proton/oxygen) ratio, 229
Hollow fiber membranes, separation of soluble products, 400–402
Hollow-fiber reactors, 445
Homologous amino acid sequences, 271
Hormones, 139
Host-vector interactions, 493–503
HPLC (high-pressure liquid chromatography), 352, 411
Hughes press, separation of insoluble products, 384
Humoral immune response, 36
Hybrid glycoforms, 129
Hybridization, 259
Hybridoma cells, 436
Hydrocarbons, metabolism of, 156–157
Hydrogen gas production, 597–598
Hydrogen macronutrient, 53
Hydrophobic chromatography (HC), 411
Hydrophobic interaction chromatography (HIC), 411
Hydroxylation, 116
Hypervariable regions, 36
Hyphae, 25
I
IEC (ion-exchange chromatography), 410–411, 414, 419–420
IEM (ion-exchange membranes), 421
Illumina sequencing, 269
IMAC (immobilized-metal-affinity chromatography), 416–419
Immobilized cell systems
active cell immobilization, 298–302
bioreactor considerations, 309–311
diffusional limitations, 304–308
encapsulation, 300
gelation of polymers, 299
ion-exchange gelation, 299
microbial flac, 305
overview, 298
passive immobilization, 303–304
polycondensation, 299
polymerization, 299
precipitation of polymers, 299
three-dimensional printing, 300
Immunoblot testing, 264
Immunotherapy, 36
Inclusion bodies, 475
Indirect methods of counting cells, 172–175
Indirect selection mutation, 250
Induced fit model, enzymes, 63
Induced pluripotent stem (iPS) cells, 529
Inducer exclusion, 131
Inducers, 130
Induction, 130
Industrial uses for
mixed culture biological waste treatment, 546–548
Industrial wastes, biological waste treatment, 549
Inhibitors, enzyme kinetics, 73–74
Initial-rate experiments, 67–68
Initiation complex, 125
Initiation factors, 125
Inner membranes
E. coli, 18
eucaryotes, 23
Insect cell–baculovirus system, 480–482
Insect cells, cultivating, 435–436
Inserting genes into DNA, 260–262
Insertion-sequence (IS) elements, 248
Integral member proteins, 43
Integral membrane in proteins, 30
Inteins, 116
Intermediate filaments, 25, 433
Internal gene transfer, 257
Internal mechanical agitation, 324–329
Internal mechanical agitation bioreactors, 324–329
Internal membrane bioreactors, 295
Interphase, 23
Intracellular spores, 20
Intrinsic concentration, 202
Ion-exchange gelation, 299
Ion-exchange membranes (IEM), 421
Ion-exchanging chromatography (IEC), 410–411, 414, 419–420
iPS (induced pluripotent stem) cells, 529
Irreversible inhibitors, enzyme kinetics, 73
IS (insertion-sequence) elements, 248
Isoelectric focusing, 420
Isoelectric precipitation, 390–392
Isofunctional enzymes, 134
Isothermal cloning, 262
J
Junk DNA. See Coding DNA.
K
Ketones, 36
Kinetics
batch cell growth. See Batch cell growth kinetics; Models of cell growth kinetics.
Michaelis–Menten. See Michaelis–Menten kinetics.
Koji process, 314
Krebs tricarboxylic acid (TCA) cycle, 149–152
L
L. lactis, 477
lacA gene, 130
Lactases, 102
Lactic acid production, 581–584
Lactose, 40
LacY enzyme, encoding, 131
lacY gene, 130
lacZ gene, 130
Lagging strands, 118
Langmuir isotherm, 404
Langmuir–Hinshelwood kinetics, 63
Latin names, 15
Leading strands, 118
LIC (ligation independent cloning), 263
Ligation independent cloning (LIC), 263
Light phase of photosynthesis, 164
Lineweaver–Burk plot, 68
Lipases, 101
Lipidation, 116
Lipids
PHA (polyhydroxyalkanoates), 44
PHB (polyhydroxybutyrate), 44
Lipoglycans. See LPS (Lipopolysaccharide).
Lipopolysaccharide (LPS), 18
Liquid fuel production, 596–597
Liquid–liquid extraction, 385–389
LLC (liquid–liquid partition chromatography), 410–411
LncRNA (long ncRNA), 49
Lock-and-key model, enzymes, 63
Logarithmic growth phase. See Exponential growth phase.
Long ncRNA (lncRNA), 49
Loop reactors, scaling up, 329–330
Lotka–Volterra model of mixed culture interactions, 542–545
Low-copy-number plasmids, 486
Lower eucaryotic cells in genetic engineering, host-vector systems, 477–479
LPS (Lipopolysaccharide), 18
LPS removal, 18
Luedeking–Piret equation, 183
Lumenal phase cytoplasm, 432
Lypophilization, purification process, 423–424
Lysogenic cells, gene transfer and rearrangement, 255
Lysogenic cycle of viruses, 17
Lysozyme, uses for, 102
Lytic cycle of viruses, 17
M
autotrophs, 52
categories of microorganisms, 52
chemautotrophs, 52
definition, 51
facultative autotrophs, 52
heterotrophs, 52
hydrogen, 53
magnesium, 53
mixotrophs, 52
oxygen, 53
phosphorus, 53
photoautotrophs, 52
potassium, 53
sulfur, 53
MAGE (multiplex automated genome engineering), 266
Magnesium, macronutrient, 53
Maintenance, 180
Maintenance coefficient, 213
Maintenance energy, 178
Mammalian cell culture, 436–437
Mammalian cells in genetic engineering, host-vector systems, 479–480
Maximum growth potential, 200–201
Medical uses for
bioprocess engineering. See Bioprocess engineering, medical uses for.
Membrane configurations, separation of soluble products, 400–402
Membrane-based units, 530
Menten, M. L., 63
Merck, producing penicillin, 5–6
Mesophiles, 14
Metabolic burden, 489
Metabolic control theory, 510
Metabolic engineering
identifying pathway enzymes, 508–509
native hosts, 508
overview, 506
Metabolic flux analysis, 510
Metabolic pathway control, 133–135
Metabolic pathways
anabolism, definition, 146
autotrophic metabolism, 163–165
biodegradation of xenobiotics (toxic aromatic compounds), 157–158
control sites in aerobic glucose metabolism, 154–155
Crabtree effect, 146
dark phase, 164
degrading compounds into simpler products. See Catabolism.
EMP (Embden–Meyerhof–Parnas) pathway, 149–152
light phase, 164
metabolic engineering, definition, 145
metabolism of hydrocarbons, 156–157
metabolism of nitrogenous compounds, 155–156
NADH, functions in biological systems, 148
nitrogen fixation, 156
nitrogenase, 156
overview, 145
Pasteur effect, 155
synthesizing complex compounds. See Anabolism.
basal level of proteins, 131
catabolite repression, 131
concerted feedback inhibition, 134
constitutive genes, 132
cooperative feedback inhibition, 134
cumulative feedback inhibition, 134
diauxic growth, 132
end-product inhibition, 133
enhancer regions, 131
enzyme induction, 131
full inhibition, 134
genetic-level control, 130–133
glucose effect, 131
inducer exclusion, 131
inducers, 130
induction, 130
isofunctional enzymes, 134
isozymes, 134
lacA gene, 130
LacY enzyme, encoding, 131
lacY gene, 130
lacZ gene, 130
metabolic pathway control, 133–135
operator regions, 130
operons, 130
permease, encoding, 131
regulons, 131
sequential feedback inhibition, 134
unregulated genes. See Constitutive genes.
Metabolism
of nutrients in animal cells, 433–434
Methane production, 564, 597–598
MF (microporous filtration), 395–398
MFCs (microbial fuel cells), 598–600
Michaelis, L., 63
vs. allosteric kinetics, 72
Michaelis–Menten kinetics, determining rate parameters
double-reciprocal plot, 68
initial-rate experiments, 67–68
interpretation of Km and Vm, 70–71
Lineweaver–Burk plot, 68
Microarrays, 270
Microbes, compared to plant cell cultivation, 457–462
Microbial flac, 305
Microbial products, classifying, 183–184
Microencapsulation, 87
Microfiltration, separation of soluble products, 395–403
categories, 54
chelating agents, 55
commonly added, 54
definition, 51
growth factors, 55
ligands, 55
rarely added, 55
Microorganisms
categories of, 52
naming, 15
Microphysiological systems, 531
Microporous filtration (MF), 395–398
Microscopic eucaryotes. See Eucaryotes, microscopic.
Microvilli, 432
Minkevich, I. G., 229
miRNA (microRNA), 49
Mitosis, 23
Mixed and forcefully aerated bioreactors, 314
Mixed culture, biological waste treatment
acid formers, 564
activated-sludge processes, 551–553
adsorbent-added activated-sludge process, 557–558
agricultural wastes, 549
Bardenpho process, 571
biological treatment, 549
BOD (biological oxygen demand), 550
CFSTR (continuous-flow, stirred-tank reactor), 552
chemical treatment, 549
COD (chemical oxygen demand), 550
contact stabilization, 557
converting wastewater to useful products, 571–572
domestic wastes, 549
fixed solids, 551
formation of methane, 564
formation of volatile acids, 564
industrial wastes, 549
MLSS (mixed-liquor suspended solids), 551
MLVSS (mixed-liquor volatile suspended solids), 551
modified activated sludge processes, 556–563
oxygen enriched air, 558
PFRs (plug flow reactors), 552
physical treatment, 549
RBC (rotating biological contactor), 561–563
solubilization of insoluble organics, 564
stop feeding/stop aeration, 556
TKN (total Kjeldahl nitrogen), 551
TOD (total organic carbon), 550
treatment, types of, 549
trickling biological filters, 558–561
types of. See also specific types.
typical steps, 551
UCT process, 571
VIP process, 571
volatilized material, 551
wastes, types of, 549. See also specific types.
wastewater characteristics, 549–551
Mixed culture, industrial uses for
SYMBA process, 548
whiskey manufacturing, 546
Mixed culture in nature, 545–546
Mixed culture interactions
commensalism, 538
competition, 536
neutralism, 537
parasitism, 539
predation, 539
same growth limiting substrate, 536–537
symbiosis, 538
Mixed culture interactions, models of
same growth limiting substrate, 540–541
Mixed inhibition, enzyme kinetics, 76
Mixed-growth-associated product formation, 183
Mixotrophic cultures, 467
Mixotrophs, 52
MLSS (mixed-liquor suspended solids), 551
MLVSS (mixed-liquor volatile suspended solids), 551
Mobile phase chromatography, 409
MoClo (molecular cloning), 263
Models of cell growth kinetics
for filamentous organisms (molds), 201
with growth inhibitors, 195–197
with time delays, 202
for transient behavior, 201–202
Modified activated sludge processes, 556–563
Molds
conidia, 25
definition, 25
fermentation method, 27
hyphae, 25
mycelium, 25
reproduction model, 26
uses for, 27
Molecular scissors, 266
Molecular sieving chromatography, 410, 414–415
Moromi culture, 314
Mortal cells, 435
Moser equation, 194
Motion, protozoa, 27
Moving-bed columns, separation of soluble products, 404
Multimers, 487
Multiorgan-on-a-chip systems, 531
Multiphase enzymatic reactions, 84–85
Multiplex automated genome engineering (MAGE), 266
Multistage chemostat bioreactor, 281–287
Mutagens, 250
Mutations. See also Gene transfer and rearrangement; Genetic engineering.
in chemostats, 217
expressed characteristics. See Phenotype.
genetic construction. See Genotype.
genotype, 248
phenotype, 248
wild type, 248
Mutations, mechanisms of genetic change
deletion mutations, 248
IS (insertion-sequence) elements, 248
nonsense mutations, 248
point mutations, 248
reading frame, 248
silent mutations, 248
suppressor mutations, 249
Mutations, selecting for desirable
chemical agents, 250
conditional mutants, 251
direct selection, 250
indirect selection, 250
mutagens, 250
natural rates of mutation, 250
replica plating, 251
selectable mutations, 250
spontaneous rates of mutation, 250
unselectable mutations, 250
Mycelium, 25
Mycoplasma, 19
N
NAD (nicotinamide adenine dinucleotide), 45
NADH, functions in biological systems, 148
NADP (nicotinamide adenine dinucleotide phosphate), 45
Naming enzymes, 61
Nanopores, 269
Native hosts, 508
Natural amino acids, 31
Natural rates of mutation, 250
Neutralism, 537
Neutrophiles, 14
Next-generation sequencing (NGS), 269
NGS (next-generation sequencing), 269
Nicotinamide adenine dinucleotide (NAD), 45
Nicotinamide adenine dinucleotide phosphate (NADP), 45
Nitrification, biological waste treatment, 567–568
Nitrogen, macronutrient, 52–53
Nitrogen fixation, 156
Nitrogenase, 156
Nitrogenous compounds, metabolism of, 155–156
N-linked glycosylation, 129
Nonanchorage-dependent cells, 435
Noncoding DNA, 49
Noncompetitive inhibitors, enzyme kinetics, 73, 74–75
Nongrowth-associated product formation, 183
Nongrowth-related functions, 181–182
Nonoccluded viruses (NOVs), 481
Nonprotein products vs. protein products, 472–474
Nonsense DNA, 122
Nonsense mutations, 248
Nonstirred reactor systems, 444–445
Normal phase chromatography, 410
NOVs (nonoccluded viruses), 481
Nucleic acids in cell construction, 44–51
Nucleoli, 433
Nucleotides. See also DNA (deoxyribonucleic acid); RNA (ribonucleic acid).
AMP (adenosine monophosphate), 45
ATP (adenosine triphosphate), 45
GTP (quanosine triphosphate), 45
major components, 45
NAD (nicotinamide), 45
NAD (nicotinamide adenine dinucleotide), 45
NADP (nicotinamide adenine dinucleotide phosphate), 45
structure of, 46
U (uracil), 45
Nucleus, eucaryotes, 22
O
Okazaki fragments, 118
Oligosaccharyltransferase (OST), 129
Open reading frames (ORFs), 271
Operator regions, 130
Operons, 130
Optical density of cell cultures, 172
ORFs (open reading frames), 271
Organized tissues, bioreactor considerations in plant cell cultivation, 466–467
Orientation effect, 63
Osmosis, separation of soluble products, 393
Osmotic shock, separation of insoluble products, 384–385
OST (oligosaccharyltransferase), 129
OTR (oxygen transfer rate), 188
OUR (oxygen uptake rate), 188
Outer membrane, E. coli, 18
Oxidation ponds, biological waste treatment, 563–564
Oxidation-reduction half-reactions, 237–240
Oxidative phosphorylation, 152–154
Oxygen
concentration for batch cell growth kinetics, 187–188
enriched air biological waste treatment, 558
macronutrient, 53
solubility, bioreactor scale-up, 332–335
Oxygen removal
dynamic method, 335
steady-state method for, 334
unsteady-state method for, 333
P
P. pastoris, 478
Packed cell volume, 172
Packed-bed bioreactors, 314
Packed-bed columns, separation of soluble products, 404
par locus, 493
Parasitism, model of mixed culture interaction, 539
Particle counters, 171
Partition coefficient, 85
Passive immobilization, 303–304
Pasteur effect, 155
Pathway enzymes, identifying, 508–509
PBPK (physiologically based pharmacokinetic) model of the human body, 531
PCR (polymerase chain reaction), 260
Pectinases, 100
WW II poster, 8
Penicillin acylase, 102
Penicillin production
bottle plant, 6
chemical synthesis, 5
schematic of, 9
Squibb, 5
submerged tank process, 6
surface method, 6
USDA Northern Regional Research Laboratory, 5–6
Peptide bond, 32
Peptides, forming from RNA. See DNA translation.
Peptidoglycan, 18
Peptidyl site, 125
Perfusion systems bioreactor, 293–294
Perinuclear space, 433
Peripheral member proteins, 43
Periplasmic space, 18
Periwinkle to ajmalicine, 465
Permease, encoding, 131
Petroff–Hausser counting chamber, 171
Pfizer, producing penicillin, 5–6
PFRs (plug flow reactors), 208, 210, 552
pH effects
batch cell growth kinetics, 186
pH effects on cells and their environments
pH values 1 or 2. See Acidophiles.
pH values 6 to 8. See Neutrophiles.
pH values above 9. See Alkaliphiles.
PHA (polyhydroxyalkanoates), 44
Phage display, 265
Phages (bacteriophages), 17
PHB (polyhydroxybutyrate), 44
Phenotype, definition, 248
Phosphoglycerides in cell construction, 43
Phospholipids in cell construction, 43
Phosphorus, macronutrient, 53
Phosphorylation, 116
Phosphotransferase system, 137
Photoautotrophs, 52
Photoperiod control, 467
Photophosphorylation, 165
Photosynthesis
bacteria, 20
carbohydrates, 36
eubacteria (true bacteria), 19
eucaryotes, 24
Phototaxis, 138
Physical environment, monitoring, 350
Physical treatment, biological waste treatment, 549
Physiologically based pharmacokinetic (PBPK) model of the human body, 531
Plant cell cultivation
aggregates, 460
anticancer agent (Taxol), 456–457
differentiated tissue, 459
friable cali, 459
plasmodesmata, 460
volumetric productivities, 468
Plant cell cultivation, bioreactor considerations
ajmalicine from periwinkle, 465
mixotrophic cultures, 467
photoperiod control, 467
root mats, 467
submerged culture, 467
Plant vs. animal eucaryotes, 22
Plasmid vectors
gene transfer and rearrangement, 254
inserting genes into DNA, 260
Plasmids
definition, 48
structural instability, 488
Plasmodesmata in plant cell cultivation, 460
Plate counts, 171
Plug flow reactors (PFRs), 208, 210, 552
Pluripotent stem cells, 529
Pneumatic conveyor dryers, purification process, 424
Point mutations, 248
Polyadenylation, 122
Polycondensation, 299
Polygenic messages, 121
Polyhydroxyalkanoates (PHA), 44
Polyhydroxybutyrate (PHB), 44
Polymerase chain reaction (PCR), 260
Polymerization, 299
Polymers, precipitating, 299
Polypeptides, amino acids in, 31
Posttranslation movement across membranes, 125
Posttranslational modification of cells, 115–116
Posttranslational modifications (PTMs), 127
Posttranslational processing, 125–129
Potassium, macronutrient, 53
Precipitation
of polymers, 299
separation of soluble products, 390–392
Precipitin, 36
Predation model of mixed culture interaction, 539
Prey–predator model of mixed culture interactions, 542–545
Primary culture of cells, 434–435
Primary metabolites, 178
Probability of extinction, 356
Probe drift, 351
Probe fouling, 351
Procaryotes. See also Eucaryotes.
archaebacteria, 15
BMCs (bacterial microcompartments), 20
definition, 15
nomenclature, 15
ribosomes, 20
shape, 18
size, 18
spores, 20
staining, 20
storage granules, 20
structures, 20
subdivisions. See Archaebacteria; Eubacteria (true bacteria).
volutins, 20
vs. eucaryotic cells, DNA transcription, 121–122
posttranslational protein release, 127
Process validation, FDA, 10–11
Progenitor cells, 529
Promoter region, 121
Prophage conversion, 256
Proteases, 100
Protective proteins, 31
Protein engineering, 266–267, 511–513
Protein products vs. nonprotein products, 472–474
Protein release, 127
Protein secretion/excretion, 476
Protein splicing, 116
Proteinogenic amino acids, 31
Proteins. See also Amino acids.
Ag (antigen) macromodule, 34, 36
basal level, 131
biological functions, 29
building blocks of, 31. See also Amino acids.
catalytic, 30
definition, 29
fibrous, 30
forming from RNA. See DNA translation.
globular, 30
humoral immune response, 36
immunotherapy, 36
integral membrane, 30
primary structure, 33
protective, 31
quaternary structure, 33
regulatory, 31
secondary structure, 33
structural, 30
structure of, 29
tertiary structure, 33
three-dimensional structure, 33–34
transport, 30
Ab (antibody) macromodule, 34
ADC (antibody-drug conjugate), 36
antibody–antigen complex, 36
antibody–antigen interaction, 36
CDRs (complementarity determining regions), 36
engineered antibodies, 36
glycans, 36
hypervariable regions, 36
Proteomics, 267
Proton/oxygen (H/O) ratio, 229
Protoplast fusion, 265
Protoplasts, 265
Protozoa
ameboid motion, 27
amoebae, 27
cilia, 27
ciliates, 27
diseases caused by, 28
flagellate motion, 27
flagellates, 27
motion, 27
sporozoans, 27
trypanosomes, 27
wastewater treatment, 28
Proximity effect, 63
Psychrophiles, 14
PTMs (posttranslational modifications), 127
Purification
freeze drying, 423
major steps in, 373
major units of operation, 372–373
pneumatic conveyor dryers, 424
rotary-drum dryers, 424
separation of soluble products, 403
spray dryers, 424
vacuum-tray dryers, 423
Purple and green bacteria. See Anoxygenic photosynthetic bacteria.
Pyrrolysine, 31
Q
Quanosine triphosphate (GTP), 45
Quasi-steady-state assumption, 66–67
Quaternary structure, proteins, 33
R
Random mutagenesis, 512
Rannie high-pressure homogenizer, 383
Rapid-equilibrium assumption, 65–66
Rarely added micronutrients, 55
Rate of substrate transfer (RST), 85
Rational design, 512
RBC (rotating biological contactor), 561–563
Reaction, integrating with separation, 424–425
Reactor. See Bioreactor.
Reading frame, 248
Reading through a terminator, 121
Recombinant DNA techniques, 258
Recovery. See also Separation.
major steps in, 373
major units of operation, 372–373
Redox potential, batch cell growth kinetics, 189
Reflection coefficient, separation of soluble products, 394
Regenerative medicine, 519–523
Registering this book, xviii
Regulated exocytosis pathway, 127
Regulatory constraints on genetic engineering, 503–506
Regulatory enzymes, 30
Regulatory proteins, 31
Regulatory RNA, 49
Regulons, 131
Rejection coefficient of an ultrafilter, 399–400
Release factor (RF), 125
Replica plating, 251
Replication
of cells, 114
DNA. See DNA replication.
origins of, 490
runaway, 490
Replication forks, 117
Reproduction model of molds, 26
Reproduction of viruses, 17
Research approaches, biologists vs. engineers, 3
Respiration
electron transport chain, 149, 152–154
glycolysis, 149
oxidative phosphorylation, 152–154
Restriction endonucleases, 253, 262–263
Retrotransposons, 115
Retroviruses. See also Viruses.
reverse transcription, 115
Reverse transcriptase, 115, 260
Reverse transcription, 115
Reversible inhibitors, enzyme kinetics, 73
RF (release factor), 125
Rho protein, 121
Ribonucleic acid (RNA). See RNA (ribonucleic acid).
Ribonucleotides, structure of, 46
Ribosomes
definition, 49
number per cell, 20
in procaryotes, 20
Ribozymes, 61
RNA (ribonucleic acid). See also DNA (deoxyribonucleic acid); Nucleic acids.
building blocks of. See Nucleotides.
carrying genetic information, 48–49
coding, 48
definition, 49
forming peptides and proteins. See DNA translation.
long ncRNA (lncRNA), 49
microRNA (miRNA), 49
mRNA splicing, 116
regulatory, 49
replication, 115
ribozymes, 61
RNA silencing, 115
RNA-dependent RNA polymerases, 115
small interfering (siRNA), 49
structure of, 47
RNA polymerase enzyme, 119
RNA silencing, 115
RNA-dependent RNA polymerases, 115
Roche 454 sequencing, 269
Rod (bacillus) cells, 14
Root mats, bioreactor considerations in plant cell cultivation, 467
Rotary vacuum precoat filters, 374
Rotary-drum dryers, purification process, 424
Rotating biological contactor (RBC), 561–563
Rotating-drum bioreactors, 314
RST (rate of substrate transfer), 85
Runaway replication, 490
Rupture with ice crystals, separation of insoluble products, 384–385
Rushton impeller, 325
S
Salting out, separation of soluble products, 390–391
Same growth limiting substrate, 536–537, 540–541
Sanger, Frederick, 267
Saturated zone, separation of soluble products, 405
SBS (sequencing by synthesis) sequencing, 269
Scenedesmus algae, 27
Secondary culture of cells, 435
Secondary metabolites, 178
Segregated models, 191
Segregation, 191
Selectable mutations, 250
Selective pressure, 489
Selenosysteine, 31
Semicontinuous bioreactors. See Fed-batch bioreactors.
Semirational design, 513
Senescence, 435
Separation, integrating with reaction, 424–425. See also Recovery.
Separation of insoluble products
cell disruption, mechanical, 383–385
cell disruption, nonmechanical, 384–385
centrifugation coefficient, 381
coagulation, 382
Dyno-Mill homogenizer, 384
flocculation, 382
French presses, 383
Gaulin–Manton presses, 383
Hughes press, 384
Rannie high-pressure homogenizer, 383
rate of filtration, 375
rotary vacuum precoat filters, 374
rupture with ice crystals, 384–385
sonicators, 383
ultrasonic vibrators, 383
X-press, 384
Separation of soluble products
adsorption zone, 405
anisotropic membranes, 395
aqueous two-phase affinity partition extraction, 389
aqueous two-phase extraction, 389–390
bed depth-service time equation, 405–409
centrifugal Podbielniak extractors, 387–388
concentration, 403
concentration polarization, 394–395
cross-flow filtration, 398–403
cross-flow ultrafiltration, 398–403
diafiltration, 403
dialysis equilibrium, 393
dissociation extraction, 387–388
Donnan equilibrium, 393
Freundlich adsorption isotherm, 403–404
hollow fiber membranes, 400–402
IEM (ion-exchange membranes), 421
ionized species. See Dissociation extraction.
isoelectric focusing, 420
isoelectric precipitation, 390–392
Langmuir isotherm, 404
liquid–liquid extraction, 385–389
membrane configurations, 400–402
MF (microporous filtration), 395–398
moving-bed columns, 404
osmosis, 393
packed-bed columns, 404
purification, 403
reflection coefficient, 394
rejection coefficient of an ultrafilter, 399–400
saturated zone, 405
solvent precipitation, 390–392
spiral-wound cartridge membranes, 400–402
tangential flow filtration, 398–403
UF (ultrafiltration), 395–398, 403
virgin zone, 405
Separation of soluble products, chromatography
ADC (adsorption chromatography), 410–411
AFC (affinity chromatography), 411, 414–419
definition, 409
displacement chromatography, 409
elution chromatography, 409
frontal chromatography, 409
gel-filtration chromatography, 410–411, 414–415
HC (hydrophobic chromatography), 411
HIC (hydrophobic interaction chromatography), 411
HPLC (high-pressure liquid chromatography), 411
IEC (ion-exchanging chromatography), 410–411, 414, 419–420
IMAC (immobilized-metal-affinity chromatography), 416–419
LLC (liquid–liquid partition chromatography), 410–411
mobile phase, 409
molecular sieving chromatography, 410
normal phase chromatography, 410
size exclusion chromatography, 410
stationary phase, 409
typical chromatographic column, 411–414
Sequencing by synthesis (SBS), 269
Sequential feedback inhibition, 134
Sexual reproduction, eucaryotes, 23
Shock loading, biological waste treatment, 552–553
Sigma factor, 119
Silent mutations, 248
Simple glycoforms, 129
Single-use bioreactors, 330–331
Single-use disposable systems, 445, 447
siRNA (small interfering RNA), 49
Site-directed mutagenesis, 512
Size exclusion chromatography, 410
Sludge bulking, biological waste treatment, 553–556
Sludge re-aeration, biological waste treatment, 556–557
Solid-state fermentation (SSF) reactors, 313–316
Solubility reduction, separation of soluble products, 390–391
Solubilization of insoluble organics, biological waste treatment, 564
Solvent precipitation, separation of soluble products, 390–392
Sometimes added micronutrients, 54–55
Sonicators, separation of insoluble products, 383
SOP (standard operating procedures), 10
Spargers, 324
Specialized transduction, gene transfer and rearrangement, 255
Sperm cells, 23
Spherical (coccus) cells, 14
Spiral (spirillum) cells, 14
Spiral-wound cartridge membranes, 400–402
Spirillum (spiral) cells, 14
Spirulina algae, 27
Spodoptera frugiperda (fall armyworm), 480
Spontaneous rates of mutation, 250
Spores of procaryotes, 20
Sporozoans, 27
Spray dryers, purification process, 424
Squibb, producing penicillin, 5
SSF (solid-state fermentation) reactors, 313–316
Stable RNA species, 121
Staining. See Gram staining.
Standard operating procedures (SOP), 10
Stationary phase chromatography, 409
Steady-state method for oxygen removal, 334
Step feeding/step aeration, biological waste treatment, 556
Steric effects on enzyme immobilization, 98
Sterility, bioreactor scale-up, 329
Sterilizing process fluids. See also Cleaning bioreactors.
continuous sterilization, 361
vs. disinfection, 356
filter sterilization, 361
glass wool filters, 362
grow-through tests, 363
probability of extinction, 356
Steroid hormone receptors, 139
Sterols, 22
Stirred-tank bioreactors for animal cell cultivation, 447
Stoichiometric calculations
elemental balances, 230
Stoichiometry by oxidation-reduction half-reactions, 237–240
Stop codons, 125
Stop signals, 121
Storage granules, procaryotes, 20
Streptokinase, uses for, 102
Streptomyces, 477
Strong promoter, 121
Strong terminators, 121
Structural proteins, 30
Structured models, 191
Submerged culture, bioreactor considerations in plant cell cultivation, 467
Submerged tank process, penicillin production, 6
Substrate inhibition, 76–79, 195
Substrate-limited growth, 192–194
Sucrose, 40
Sulfation, 116
Sulfur, macronutrient, 53
Suppressor mutations, 249
Surface method of penicillin production, 6
Suspended animal cell cultures, 447
Suspension cultures
bioreactor considerations in plant cell cultivation, 462–463
in plant cell cultivation, 458–459
Symbiosis, model of mixed culture interaction, 538
Synonymous mutations, 259
Systems biology, 29, 267, 509–511. See also Genomics.
T
TA cloning, 262
Taq (Thermus aquaticus), 14
Taxonomy of cells. See Cell taxonomy.
TCA (Krebs, tricarboxylic acid) cycle, 149–152
Teichoic acids, 19
Telomere synthesis, 115
Temperate phages, 256
Temperature effects, batch cell growth kinetics, 184–185
Temperature inactivation, 83
Tessier equation, 194
Testing for proteins, 264
Tetramers, 487
Thermal denaturation, 83
Thermoacidophiles, 21
Thermodynamic equilibrium and cell death, 51
Thermodynamics of biological reactions, 240–242
Thermophiles, 14
Thermus aquaticus (Taq), 14
Three-dimensional printing of living cells, 300
Three-dimensional structure, proteins, 33–34
Thylakoids, 24
TKN (total Kjeldahl nitrogen), 551
TOD (total organic carbon), 550
TOPO cloning, 262
Total Kjeldahl nitrogen (TKN), 551
Total organic carbon (TOD), 550
Totipotency in plant cell cultivation, 457–461
Toxic aromatic compounds (biodegradation of xenobiotics), 157–158
Transcription terminators, 121
Transcriptomics, 270
Transduction, gene transfer and rearrangement, 254–256
Transformation, gene transfer and rearrangement, 254
Transformed cells, 435–436, 479
Transgenic plants and animals, 482–484
Transport proteins, 30
Transport vesicle fusion, 127
Transposons, gene transfer and rearrangement, 257
Tray bioreactors, 314
Trickling biological filters, biological waste treatment, 558–561
Tricoplusia ni (cabbage looper), 480
True bacteria (eubacteria)
evolution of, 15
Gram staining, 18
photosynthesis, 19
Trypanosomes, 27
Trypsin, uses for, 102
Tubulin, 25
Turbidity, 172
Two-dimensional gel electrophoresis, 270
Two-phase fermentation, 489
U
U (uracil), 45
Ubiquitination, 116
Ubiquitins, 116
UCT process for biological waste treatment, 571
UF (ultrafiltration), separation of soluble products, 395–398, 403
Ultrasonic vibrators, separation of insoluble products, 383
Unbalanced growth, 191
Uncompetitive inhibitors, enzyme kinetics, 75–76
Union Carbide, 552
Units, 70
UNOX process for biological waste treatment, 552, 558
Unselectable mutations, 250
Unstable RNA species, 121
Unsteady-state method for oxygen removal, 333
Unstructured nonsegregated models, 192–201
Unwinding enzymes, 117
Uracil (U), 45
USDA Northern Regional Research Laboratory, 5–6
V
Vacuoles, 24
Vacuum-tray dryers, purification process, 423
van der Waals forces, 63
Variable-volume continuous culture bioreactors. See Fed-batch bioreactors.
VEFCS (very enriched fructose corn syrup) production, 595
Viable cell count, 171
VIP process for biological waste treatment, 571
Viral gene delivery systems, 524
Viral infection, models of, 524–527
Virgin zone, separation of soluble products, 405
Viruses. See also HIV (human immunodeficiency) virus; Retroviruses.
capsid coating, 17
classifying, 15
definition, 16
infecting bacteria. See Phages.
lysogenic cycle, 17
lytic cycle, 17
mode of reproduction, 17
size, 16
that infect bacteria. See Phages.
Volatile acid formation, biological waste treatment, 564
Volatilized material, biological waste treatment, 551
Volumetric productivities in plant cell cultivation, 468
Volutins in procaryotes, 20
W
Wastes, types of, 549
Wastewater treatment. See also Mixed culture biological waste treatment.
algae for, 27
converting to useful products, 571–572
protozoa for, 28
Weak terminators, 121
Western blot testing, 264
Whiskey manufacturing, 546
Wild type mutations, 248
Working volume, bioreactor scale-up, 328
X
Xenobiotics biodegradation (toxic aromatic compounds), 157–158
X-press, separation of insoluble products, 384
Y
Yamanaka, Shinaya, 529
Yeast-mediated cloning, 263
Yeasts
definition, 25
in genetic engineering, host-vector systems, 478
reproductive modes, 25
Saccharomyces cerevisiae, 25–26
Yield coefficients
theoretical predictions, 235–236
Yield factors for aerobic growth, 182
Z
Zwitterion, 32
Zygotes, 23
Zymomonas, 161