bluuebunny/crossref_metadata_2025 huggingface dataset:
On the Pathogenicity of Autoantigen-Specific T-Cell Receptors
Authors: Burton Amanda R. , Vincent Erica , Arnold Paula Y. , Lennon Greig P. , Smeltzer Matthew , Li Chin-Shang , Haskins Kathryn , Hutton John , Tisch Roland M. , Sercarz Eli E. , Santamaria Pere , Workman Creg J. , Vignali Dario A.A.
Published: February 2008

OBJECTIVE—Type 1 diabetes is mediated by T-cell entry into pancreatic islets and destruction of insulin-producing β-cells. The relative contribution of T-cells specific for different autoantigens is largely unknown because relatively few have been assessed in vivo.

RESEARCH DESIGN AND METHODS—We generated mice possessing a monoclonal population of T-cells expressing 1 of 17 T-cell receptors (TCR) specific for either known autoantigens (GAD65, insulinoma-associated protein 2 (IA2), IA2β/phogrin, and insulin), unknown islet antigens, or control antigens on a NOD.scid background using retroviral-mediated stem cell gene transfer and 2A-linked multicistronic retroviral vectors (referred to herein as retrogenic [Rg] mice). The TCR Rg approach provides a mechanism by which T-cells with broad phenotypic differences can be directly compared.

RESULTS—Neither GAD- nor IA2-specific TCRs mediated T-cell islet infiltration or diabetes even though T-cells developed in these Rg mice and responded to their cognate epitope. IA2β/phogrin and insulin-specific Rg T-cells produced variable levels of insulitis, with one TCR producing delayed diabetes. Three TCRs specific for unknown islet antigens produced a hierarchy of insulitogenic and diabetogenic potential (BDC-2.5 > NY4.1 > BDC-6.9), while a fourth (BDC-10.1) mediated dramatically accelerated disease, with all mice diabetic by day 33, well before full T-cell reconstitution (days 42–56). Remarkably, as few as 1,000 BDC-10.1 Rg T-cells caused rapid diabetes following adoptive transfer into NOD.scid mice.

CONCLUSIONS—Our data show that relatively few autoantigen-specific TCRs can mediate islet infiltration and β-cell destruction on their own and that autoreactivity does not necessarily imply pathogenicity.
Linear gradings of polynomial algebras
Authors: Jędrzejewicz Piotr
Published: February 2008

Let k be a field, let $$
G
$$ be a finite group. We describe linear $$
G
$$-gradings of the polynomial algebra k[x
1, ..., x
m] such that the unit component is a polynomial k-algebra.
Compact corigid objects in triangulated categories and co-t-structures
Authors: Pauksztello David
Published: February 2008

In the work of Hoshino, Kato and Miyachi, [11], the authors look at t-structures induced by a compact object, $$
C
$$, of a triangulated category, $$
\mathcal{T}
$$, which is rigid in the sense of Iyama and Yoshino, [12]. Hoshino, Kato and Miyachi show that such an object yields a non-degenerate t-structure on $$
\mathcal{T}
$$ whose heart is equivalent to Mod(End($$
C
$$)op). Rigid objects in a triangulated category can the thought of as behaving like chain differential graded algebras (DGAs). Analogously, looking at objects which behave like cochain DGAs naturally gives the dual notion of a corigid object. Here, we see that a compact corigid object, $$
\mathcal{S}
$$, of a triangulated category, $$
\mathcal{T}
$$, induces a structure similar to a t-structure which we shall call a co-t-structure. We also show that the coheart of this non-degenerate co-t-structure is equivalent to Mod(End($$
\mathcal{S}
$$)op), and hence an abelian subcategory of $$
\mathcal{T}
$$.
Transformations preserving the Hausdorff-Besicovitch dimension
Authors: Albeverio Sergio , Pratsiovytyi Mykola , Torbin Grygoriy
Published: February 2008

Continuous transformations preserving the Hausdorff-Besicovitch dimension (“DP-transformations”) of every subset of R
1 resp. [0, 1] are studied. A class of distribution functions of random variables with independent s-adic digits is analyzed. Necessary and sufficient conditions for dimension preservation under functions which are distribution functions of random variables with independent s-adic digits are found. In particular, it is proven that any strictly increasing absolutely continuous distribution function from the above class is a DP-function. Relations between the entropy of probability distributions, their Hausdorff-Besicovitch dimension and their DP-properties are discussed. Examples are given of singular distribution functions preserving the fractal dimension and of strictly increasing absolutely continuous functions which do not belong to the DP-class.
Holomorphic triples of genus 0
Authors: Pasotti Stefano , Prantil Francesco
Published: February 2008

Here we study the relationship between the stability of coherent systems and the stability of holomorphic triples over a curve of arbitrary genus. Moreover we apply these results to study some properties and give some examples of holomorphic triples on the projective line.
Vector bundles on Hirzebruch surfaces whose twists by a non-ample line bundle have natural cohomology
Authors: Ballico Edoardo , Malaspina Francesco
Published: February 2008

Here we study vector bundles E on the Hirzebruch surface F
e such that their twists by a spanned, but not ample, line bundle M = $$
\mathcal{O}
$$
Fe(h + ef) have natural cohomology, i.e. h
0(F
e, E(tM)) > 0 implies h
1(F
e, E(tM)) = 0.
On the exact values of coefficients of coiflets
Authors: Černá Dana , Finěk Václav , Najzar Karel
Published: February 2008

In 1989, R. Coifman suggested the design of orthonormal wavelet systems with vanishing moments for both scaling and wavelet functions. They were first constructed by I. Daubechies [15, 16], and she named them coiflets. In this paper, we propose a system of necessary conditions which is redundant free and simpler than the known system due to the elimination of some quadratic conditions, thus the construction of coiflets is simplified and enables us to find the exact values of the scaling coefficients of coiflets up to length 8 and two further with length 12. Furthermore for scaling coefficients of coiflets up to length 14 we obtain two quadratic equations, which can be transformed into a polynomial of degree 4 for which there is an algebraic formula to solve them.
A numerically stable least squares solution to the quadratic programming problem
Authors: Übi E.
Published: February 2008

The strictly convex quadratic programming problem is transformed to the least distance problem — finding the solution of minimum norm to the system of linear inequalities. This problem is equivalent to the linear least squares problem on the positive orthant. It is solved using orthogonal transformations, which are memorized as products. Like in the revised simplex method, an auxiliary matrix is used for computations. Compared to the modified-simplex type methods, the presented dual algorithm QPLS requires less storage and solves ill-conditioned problems more precisely. The algorithm is illustrated by some difficult problems.
Wolbachia-mediated reproductive alterations in invertebrate hosts and biocontrol implications of the bacteria: an update
Authors: Islam M Saiful
Published: February 2008

Wolbachia are obligatory intracellular bacteria that have evolved to manipulate reproduction and/or metabolism of their arthropod and nematode hosts in a number of ways, all designed to the benefit of their own survival and transmission through hosts populations. An updated account of the occurrence, identification, phylogeny and genetics, phenotypic effects, distribution, mechanisms of action, horizontal transmission, infection dynamics, evolutionary consequences and biocontrol implications of the bacteria are presented. Associations between these maternally heritable bacteria and their hosts not only cover the entire range of interactions from parasitism to mutualism but also a complex interplay of both. Wolbachia are transmitted vertically from mothers to offspring, and also horizontally within or between arthropod taxa. They are known to induce cytoplasmic incompatibility (CI) via unviable brood, parthenogenesis induction (PI) through asexual reproduction, feminization (F) by converting males into functional females, and male killing (MK) by causing death to sons of the infected mothers. How these bacteria influence host fitness and population dynamics, and could play an important role in speciation have been reviewed. Possible uses of the bacteria and their predominant phenotypes in control programmes for agricultural pests and human disease vectors have been discussed.

Key words: Wolbachia, reproductive manipulation, cytoplasmic incompatibility, parthenogenesis induction, feminization, male killing, biocontrol implications

Univ. j. zool. Rajshahi Univ. Vol. 26, 2007. pp. 1-19
Induced Breeding of Pila globosa (Swainson 1822) (Gastropoda: Prosobranchia) for Commercial Farming
Authors: Jahan Md Sarwar , Islam Md Refiqul , Rahman Md Redwanur , Alam M Manjurul
Published: February 2008

Studies were made on the number of egg clutch, copulating pairs, duration of mating, duration of egg laying, and weight of egg clutch of Pila globosa by inducing it with Pituitary Gland (PG) and Optic Tentacle cut (OT) under laboratory condition. The effect of inducing the animal with PG and OT cut showed that it resulted in an increase in the number of egg clutch in comparison with that of the control.

In control animals the number of egg clutch was found to be 0.30±0.02 which was 20.93% of total egg clutches laid. Whereas in animals with Pituitary Gland (PG) and Optic Tentacles (OT) cut the number of egg clutch were 0.43±0.61 and 0.70±0.86 which were 30.23% and 48.83% of total egg clutches laid respectively. The animals injected with pituitary gland extract and optic tentacle cut showed an increase in the number of egg clutch in comparison with that of the control animals.

In control animals, duration of mating, duration of egg laying, and weight of egg clutch were found as, 3.23±0.29hrs., 5.37±1.51hrs., and 8.38±g respectively. The pituitary gland (PG) injected and optic tentacle (OT) cut, duration of mating, duration of egg laying and weight of egg clutch were found as, 3.52±0.26hrs., 4.64±1.63hrs., and 8.54±2.10g.; 3.51±0.33hrs., 5.47±1.19hrs., and 8.45±2.53g respectively.

Key words: Pila globosa, induced breeding, Commercial Farming.

Univ. j. zool. Rajshahi Univ. Vol. 26, 2007. pp. 35-39
Combined effect of UV-radiation and triflumuron on the progeny of Alphitobius diaperinus (Panzer)(Coleoptera: Tenebrionidae) at different storage period
Authors: Begum Mahmuda , Parween Selina , Faruki Saiful Islam
Published: February 2008

Eggs of the lesser mealworm, Alphitobius diaperinus (Panzer) were exposed to UV-rays of 254nm wavelength for different durations viz. 1, 2, 4 and 8 minutes. After seven days of hatching, larvae of each exposure were reared separately on triflumuron (1 x 10-3 mg/kg) treated food and observed the population of various developmental stages e.g., egg, larval, pupal and adult at storage periods of 3-, 6- and 9-months. UVrays and triflumuron treatments deleteriously reduced the populations of all the developmental stages of A. diaperinus. Egg and pupal populations of the beetle were adversely influenced by the storage periods also. Complete reduction of A. diaperinus populations was achieved from 6-9 months storage periods, when eggs were exposed to UV-rays for 8 minutes.

Key words: Mealworm, UV-rays, IGR, progeny production

Univ. j. zool. Rajshahi Univ. Vol. 26, 2007. pp. 45-48
A comparative study on reproductive performance and productivity of the Black Bengal and Crossbred goat at Atrai, Bangladesh
Authors: Hassan Mohammad Mahmudul , Mahmud SM Niaz , Islam SKM Azizul , Miazi Omar Faruk
Published: February 2008

The present investigation was carried out to detect the status of different productive and reproductive parameters of Black Bengal and Crossbred goats at Bandaikhara village under Atrai Upazilla of Naogaon district during the period of September to December/2005. The average age at first sign of heat of Black Bengal goats was better than that of Crossbred goats. In Black Bengal goat the average age at first kidding was 360.5±10 days, whereas, in crossbred goats it was 411.5±15.5 day. Significantly (P<0.01) lower the post partum heat period in Black Bengal goat than the crossbred goat. The average kidding interval in Black Bengal and Crossbred goats were 179±20 and 270±22 days respectively and differences are statistically significant (P<0.01). The usual numbers of kids at one time in Black Bengal goats vary from single to quadruplet. On the other hand, litter size of crossbred goat was single or twin. The average birth weight of Black Bengal goat was lower than Crossbred goats, which are statistically significant (P<0.05). The average body weight gain after 365 days is better in Crossbred than Black Bengal goats and statistically significant (P<0.01). The average milk yield in Crossbred goat was 1.05 liter/day, whereas, in Black Bengal goat, it produces milk that only nourished its kids. It was concluded that the reproductive performance like early maturity, larger litter size, shorter postpartum period, minimum kidding interval are better in Black Bengal goat. On the other hand productive performance like higher birth weight, maximum body weight gain, high milk yield, longer lactation length are suitable in crossbred goat.

Key words: Black Bengal goat, Crossbred goat, Production, Reproduction, Performance

Univ. j. zool. Rajshahi Univ. Vol. 26, 2007. pp. 55-57
The lymphocystis diseases in the Olive flounder, Paralichthys olivaceus
Authors: Hossain Mosharrof , Kim Seok Ryel , Oh Myung Joo
Published: February 2008

Lymphocystis disease virus (LCDV) is the causative agent of lymphocystis disease, affecting more than 100 teleost species worldwide. Characteristically, LCD is chronic, self limiting and species specific. The greatly hypertrophied cells, called lymphocystis tumor cells, typically occur on the skin, fins and oral region. Lymphocystis cells were ovoid to circular and varied in sizes ranging from 200-250 mm. The lymphocystis disease infected flounder have unsightly appearances that discourage the commercial values. A PCR detection technique was developed to amplify a fragment of LCDV major capsid protein gene (1347bp) which is shortcoming and useful. The PCR result proved that the LCD-virus replicated in the epidermis (fins and skin) not in the spleen, kidney, intestine or brain of Paralichthys olivaceus.

Keyword: Lymphocystis disease, LCDV, PCR, Paralichthys olivaceus

Univ. j. zool. Rajshahi Univ. Vol. 26, 2007. pp. 59-62
Contact and Fumigant Toxicity of Essential Oils Against Callosobruchus maculatus
Authors: Mahfuz I , Khalequzzaman M
Published: February 2008

Toxicity of five essential oils (EOs), viz. cardamom, cinnamon, clove, eucalyptus and neem oils were investigated against the cowpea weevil, Callosobruchus maculates (Fab.) adults, through contact and fumigation bioassay. In the contact bioassay eucalyptus oil was found to be the most effective in inducing mortality both after 24 and 48 h of treatments. The toxicity of the oils followed in the order: eucalyptus > clove > cinnamon > cardamom > neem. In the fumigation bioassay, however, a reverse result was obtained with eucalyptus oil where it shows the last position for 24 h and fourth position for 48 h after treatments. The efficacy in respect of the toxicity followed in the order: clove > cinnamon > cardamom > neem > eucalyptus after 24 h after treatment, and clove > cinnamon > cardamom > eucalyptus > neem after 48 h after treatments.

Keywords: Essential oil, bioassay, LD50, C. maculates

Univ. j. zool. Rajshahi Univ. Vol. 26, 2007. pp. 63-66
Productive and reproductive performance of crossbred and indigenous Dairy cows under rural conditions in Comilla, Bangladesh
Authors: Miazi Omar Faruk , Hossain Md Emran , Hassan Mohammad Mahmudul
Published: February 2008

A comparative account of the productive and reproductive performance of crossbred and indigenous dairy cows at some selected areas of Comilla district. The survey was conducted on 50 dairy cows for a period of four months from June to September, 2004. Out of 50 cows 25 were crossbred and 25 were indigenous. Results showed that the average daily milk production of Local, Shahiwal x Local, Friesian x Local and Jersey x Local dairy cows was 2.26±0.19, 4.9±0.95, 6.0±1.0 and 5.71±0.87 liter respectively. The average age of calving interval and lactation length of the crossbred and indigenous cows did not differ significantly (P>0.05). However, the average age at puberty of Shahiwal x Local, Friesian x Local and Jersey x Local was significantly (P<0.01) lower than the local breed. The crossbred cows had significantly (P<0.01) lower pubertal age than local. The postpartum heat period and service per conception of different crossbred and local cows did not differ significantly (P>0.05). The average gestation length of Local, Shahiwal x Local, Friesian x Local and Jersey x Local was 289.88±1.44, 285.0±0.0, 285.0±4.18, and 282.08±2.42 days respectively. The productive and reproductive performance of Friesian x Local cows was superior to the rest of the breeds under study.

Key words: Dairy cows, indigenous, crossbred, production, reproduction and performance

Univ. j. zool. Rajshahi Univ. Vol. 26, 2007. pp. 67-70
Developmental stages of red the spider mite, Oligonychus coffeae Neitner (Acari: Tetranychidae) infesting rose
Authors: Haque M , Wahab A , Naher N , Begum Afroza
Published: February 2008

The experiment was conducted to study the duration of different developmental stages of Oligonychus coffeae Nietner in six generations in different seasons of the year. The eggs of O. coffeae developed to adult within the shortest duration of 5.30±0.16 days at 30.28°C and 76.00% RH in June, but it took 12.91±0.21 days at 19.80°C and 75.41% RH in January. The highest temperature accelerated the developmental rate and reduced the duration of developmental stages. Temperature exerted significant effect on all the developmental stages of O. coffeae except deutonymph. But the relative humidity had no significant effect except deutonymph.

Key words: Developmental stages, red spider mite, Oligonychus coffeae rose

Univ. j. zool. Rajshahi Univ. Vol. 26, 2007. pp. 71-72
Effect of inorganic fertilizer on the fish growth and production in polyculture system of Bangladesh
Authors: Sayeed MA , Alam MT , Sultana S , Ali MS , Azad MS , Islam MA
Published: February 2008

A study was carried out on the optimal dose of inorganic fertilizer used in carp polyculture system over a period of 10 months. Three treatments were assigned: without inorganic fertilizer, with the application of 100 kg/ha/month inorganic fertilizer and 150 kg/ha/month inorganic fertilizer as T1, T2 and T3, respectively. Each treatment had three replications. The selected indigenous carp species were Rui (Labeo rohita), Catla (Catla catla) and Mrigal (Cirrhinus mrigala), and exotic carp species were silver carp (Hypophthalamichthys molitrix), grass carp (Ctenopharyngodon idella), common carp (Cyprinus carpio) and thai sarpunti (Barbodes gonionotus). The average water area of the experimental ponds was 0.11±0.01 ha and average depth of water in all ponds was 1.26 m. The treatments showed no effect on water temperature, dissolved oxygen, alkalinity and pH. The fish production was significantly higher (P>0.05) in both the treatments T2 and T3 than that of T1 where no inorganic fertilizer was used. But there was no significant difference between T2 and T3 and T2 was with lower dose inorganic fertilizer (100 kg/ha/month) than T3. Therefore, 100 kg/ha/month inorganic fertilizers may be suggested in carp polyculture system for better production.

Key words: Inorganic fertilizer, optimal dose, Polyculture, Fish production.

Univ. j. zool. Rajshahi Univ. Vol. 26, 2007. pp. 77-80
Efficacy of edible oils in the control of pulse beetle, Callosobruchus chinensis L. in stored pigeonpea
Authors: Khalequzzaman M , Mahdi Shah Hussain Ahmad , Goni SHM Osman
Published: February 2008

Seven vegetable oils viz., sunflower (Heliunthus annus, L.), mustard (Brassica juncea Cross ), groundnut (Arachis hypogaea, L.), sesame (Sesamum indicum L.), soybean [Glycine max L. (Merril)], olive (Olea europea) and oil palm (Elaeis guineensis W. J. Jacquin), each were applied at the rates of 5, 7.5, and 10 ml.kg-1 of grain (0.5, 0.75 and 1% v/w concentrations) as grain protectants of pigeonpea against the pulse beetles (Callosobruchus chinensis L.). Effects on progeny emergence, loss in grain weight, and germination up to 66 days after treatment were measured. Adult emergence was completely prevented and the minimum grain loss was achieved by groundnut oil at 1% up to 66 days after treatment. Since treatments with groundnut and palm oils at 5 ml.kg-1 showed high acceptability by consumers, it can be recommended for C. chinensis control in stored pigeonpea for approximately two months.

Key Words: Vegetable oils, Callosobruchus, pigeonpea, progeny emergence, grain protectant

Univ. j. zool. Rajshahi Univ. Vol. 26, 2007. pp. 89-92
Effect of Bishkatali, Polygonum hydropiper L. plant extracts against the red flour beetle, Tribolium castaneum Herbst
Authors: Kundu BR , Ara R , Begum MM , Sarker ZI
Published: February 2008

Toxicity, repellency and residual effects of Bishkatali plant extracts in chloroform and ethyl alcohol solvents were evaluated against the red flour beetle. Five concentrations viz. 500, 250, 125, 62.5 and 31.25mg/ml of Bishkatali plant extracts of both solvents were used in the experiment. The plant extracts in both solvents were moderately toxic to Tribolium castaneum. The toxicity of ethyl alcohol extract was more than chloroform extract after 24 and 72 hours treatment on the insect. Bishkatali plant extract in both solvents showed strong repellency against T. castaneum in which chloroform extract was better than ethyl alcohol extract. The rate of repellency was increased with the increment of concentration. Both the extracts have produced remarkable residual effect in reducing the progeny of T. castaneum. The lowest numbers of F1 adult progeny (32.7, 25.3 and 27.0) emerged from the wheat flour treated with 500mg/10g chloroform extract when parent released at 7, 12, 17 days after treatment respectively. Whereas with 500mg/10g ethyl alcohol extract, 38.0, 29.7 and 30.3 F1 adult progeny emerged when parents released at 7, 12, 17 days after treatment respectively. Bishkatali plant extracts in both chloroform and ethyl alcohol had remarkable residual effects on T. castaneum by reducing the production of F1 progeny and/or by increasing the population mortality.

Key words: Botanical, solvent, red flour beetle, mortality, progeny, repellency, residual

Univ. j. zool. Rajshahi Univ. Vol. 26, 2007. pp. 93-97
Chemotherapy- and Cancer-Related Nausea and Vomiting
Authors: Warr David G.
Published: February 2008

Approximately one half of cancer patients will experience nausea or vomiting during the course of their disease either because of the cancer itself or because of their treatment. Emesis attributable to cancer warrants a careful investigation to determine whether a treatable underlying cause is responsible. Interventions using dexamethasone and octreotide may reduce vomiting attributable to bowel obstruction. In the absence of a bowel obstruction or a correctable cause, the usual approach is a sequential trial of antiemetics guided by considerations of cost and side effects. Major progress in managing chemotherapyinduced emesis followed from the use of a combination of a corticosteroid and 5-hydroxytryptamine3 (5-HT3) receptor antagonist for moderately to highly emetogenic chemotherapy. Nevertheless, vomiting still occurred in approximately 40% of women receiving chemotherapy containing an anthracycline plus cyclophosphamide and in approximately 50% of patients receiving high-dose cisplatin. The addition of aprepitant, a neurokinin 1 receptor antagonist, improved control of emesis by a further 15%–20%, and that agent is now recommended as part of standard antiemetic therapy for patients at high risk of emesis. Based largely on anecdotal experience, cannabinoids and olanzapine are sometimes also recommended in patients with refractory emesis. Phase III trials are required to confirm their efficacy as addons to a corticosteroid, a 5-HT3 receptor antagonist, and possibly aprepitant.
Measurement of Aminoacylases
Authors: Pushkin Alexander , Kurtz Ira
Published: February 2008

The unit describes the assays for aminoacylase activity, with specific emphasis on aminoacylase III. The methods are based on the determination of deacetylated products of the aminoacylase‐catalyzed reactions in fluorescence and absorbance assays. The unit also provides methods for isolation of the aminoacylase III from tissues and bacterial or mammalian cells and subsequent purification and analysis.Curr. Protoc. Toxicol. 35:6.14.1‐6.14.20. © 2008 by John Wiley & Sons, Inc.
Experimental Models of Hypoxic‐Ischemic Encephalopathy: Hypoxia‐Ischemia in the Immature Rat
Authors: Carloni Silvia , Balduini Walter
Published: February 2008

The development of experimental models to study the mechanisms of perinatal hypoxic‐ischemic encephalopathy and stroke and effective therapies represents an important goal in perinatal medicine. However, due to the complexity of this pathological condition in humans, to date there is no ideal animal model that completely reproduces this condition. This unit describes the most widely used rodent animal model for the study of hypoxic‐ischemic encephalopathy during development. The model consists of 7‐day‐old pup rats subjected to unilateral carotid artery ligation followed by timed hypoxia exposure, and incorporates both focal cerebral ischemia and reperfusion. Its strength lies in the relative ease of the surgical procedure, the low mortality rate, and the possibility of performing long‐term experiments, a necessity for preclinical therapeutic trials. Over the years, this model has been extensively characterized, and most information on the mechanisms responsible for neurodegeneration and possible therapeutic approaches following hypoxia‐ischemia during brain development derives from studies performed using this model. Curr. Protoc. Toxicol. 35:11.15.1‐11.15.11. © 2008 by John Wiley & Sons, Inc.
The Syrian Hamster Embryo (SHE) Low pH Cell Transformation Assay
Authors: Pant Kamala , Aardema Marilyn J.
Published: February 2008

The Syrian hamster embryonic (SHE) cell transformation assay (CTA) at pH 6.7 can determine the ability of a test article to induce morphological transformation (MT) in cultured SHE cells. The assay uses SHE cells prepared at gestation day ∼13 and frozen. Target cells are seeded onto a layer of feeder cells (X‐ray irradiated SHE cells) and treated with test article for 24 hr or 7 days. After a growth period of 7 days, the cells are fixed, stained, and evaluated for MT. Normal colonies typically contain a monolayer of cells with an organized, often flowing, pattern of growth and minimal cell criss‐crossing at a confluent density. Transformed colonies contain randomly oriented, stacked cells, with cell criss‐crossing throughout the colony. The transformed cells are frequently more basophilic than their normal counterparts, with increased nuclear/cytoplasmic ratios. This assay provides a valuable tool for evaluating the carcinogenic potential of a test article. Curr. Protoc. Toxicol. 35:20.3.1‐20.3.16. © 2008 by John Wiley & Sons, Inc.
MultiBac: Multigene Baculovirus‐Based Eukaryotic Protein Complex Production
Authors: Bieniossek Christoph , Richmond Timothy J. , Berger Imre
Published: February 2008

Multiprotein complexes are an emerging focus in current biology, resulting in a demand for advanced heterologous expression systems. This unit provides protocols for the expression of eukaryotic multiprotein complexes using multigene expression vectors. Homologous and site‐specific recombinases facilitate their assembly. Thus, modification of individual subunits for revised expression studies is achieved with comparative ease. The strategy outlined here employs the MultiBac baculoviral expression system for multiprotein complexes as an example. Baculoviral expression does not require particular safety precautions due to the replication incompetence of baculovirus in mammalian hosts. The MultiBac system provides for improved protein production due to deletion of specific viral genes (V‐cath, chiA). Most of the steps described in this unit are tailored for high‐throughput approaches. The general strategy of rapidly combining encoding DNAs by recombination into multigene expression vectors for protein complex expression can also be applied to other prokaryotic or mammalian expression systems. Curr. Protoc. Protein Sci. 51:5.20.1‐5.20.26. © 2008 by John Wiley & Sons, Inc.
Phage Display for Generating Peptide Reagents
Authors: Brigati Jennifer R. , Samoylova Tatiana I. , Jayanna Prashanth K. , Petrenko Valery A.
Published: February 2008

This unit presents detailed protocols for selection and propagation of landscape phages, which are fusions of filamentous phage fd (or its close relatives M13 and f1) and foreign DNA that result in chimeric phage virions with foreign peptides (8 to 9 amino acids long) covering the entire surface of the phage particles. These landscape phages bind specifically to mammalian and bacterial cells, spores, or discrete molecular targets. Curr. Protoc. Protein Sci. 51:18.9.1‐18.9.27. © 2008 by John Wiley & Sons, Inc.
Utilizing Peptide SPOT Arrays to Identify Protein Interactions
Authors: Cushman Ian
Published: February 2008

SPOT arrays consist of synthesized peptides 12‐ to 18‐amino acids long, with overlapping sequences that cover the entire sequence of a protein, covalently linked to a solid support. This unit describes how to construct peptide SPOT arrays, biotinylate recombinant proteins, and conduct overlay assays to identify binding interactions. In addition, directions describing how to analyze results to determine single amino acid binding contributions are included. The two techniques in this unit describe how to scan protein sequences to find binding motifs and how to conduct site‐directed mutagenesis studies. Curr. Protoc. Protein Sci. 51:18.10.1‐18.10.9. © 2008 by John Wiley & Sons, Inc.
Carcinoembryonic Antigen Transgenic Mouse Models for Immunotherapy and Development of Cancer Vaccines
Authors: Bhattacharya‐Chatterjee Malaya , Saha Asim , Foon Kenneth A. , Chatterjee Sunil K.
Published: February 2008

The goal of cancer therapy remains as the long‐term eradication of tumor cells without adverse effects on normal tissue. Conventional approaches utilizing chemotherapy and radiotherapy are limited by both their toxicity and lack of specificity. In recent years, investigators have carried out several studies designed to evaluate whether human tumor‐associated antigens (TAAs) can be exploited as targets for immunotherapy, specifically for human cancer vaccine development. A major limitation in immunotherapy studies of human cancer is the general lack of appropriate preclinical models. Clinical studies can be difficult to implement, particularly when a clear understanding of the potential efficacy, limitation, and safety of an immunotherapeutic strategy is not available from relevant animal investigations. However, mice carrying a transgene for a human tumor self‐antigen may provide a more acceptable experimental model in which knowledge about immunotherapeutic strategies aiming at the TAA of interest can be enhanced prior to initiating clinical trials. Since the different strategies in experimental immunotherapy of cancer have been directed to activate different immune system components, a variety of transgenic mouse models have been generated expressing either TAA, human leukocyte antigen (HLA), oncogene, or immune effector cell molecules. These models may serve as an excellent platform for the identification of novel targets for immunotherapy as well as to evaluate the efficacy of targeted therapies and will lead to the development of clinical trials for cancer patients. In this unit, a brief overview of the generation and study of different vaccine approaches in carcinoembryonic antigen (CEA) transgenic mouse models and the experimental findings in mouse models that spontaneously develop gastrointestinal tumors and express the CEA transgene is provided. Curr. Protoc. Immunol. 80:20.8.1‐20.8.12. © 2008 by John Wiley & Sons, Inc.
Aminoacyl tRNASynthetases, Chemistry of
Authors: Nawaz Mir Hussain , Martinis Susan A.
Published: February 2008

Aminoacyl‐tRNA synthetases (aaRSs) compose a family of essential enzymes that attach amino acids covalently to tRNA molecules during protein synthesis. Some aaRSs possess a hydrolytic amino acid editing function to ensure the fidelity of protein synthesis. In addition, aminoacylation can occur by indirect pathways that rely on mischarged tRNA intermediates and enzymes other than aaRSs. Throughout evolution, structural and functional divergence of aaRSs has yielded diverse secondary roles. Likewise, aaRS‐like proteins with either sequence or structural similarities to synthetases exhibit functions that may or may not be related to aminoacylation. Many of these diverse aaRSs and aaRS‐like proteins have been capitalized on by the microbial world and by medical research as targets for therapeutic agents such as antibiotics.
BacterialDNAPolymerases, Chemistry of
Authors: Pomerantz Richard T. , O'Donnell Mike
Published: February 2008

All DNA polymerases share a common two‐metal ion catalyzed chemistry of nucleotide incorporation. Structure analysis, however, suggests that DNA polymerases share one of two different ancestors, which converged to employ the same mechanism.Escherichia coli, the prototypical bacterium, encodes five different DNA polymerases. The chromosomal replicase functions closely with clamps, clamp‐loaders, and other proteins. Oxidative damage to DNA during normal cell growth requires interplay among the several distinct DNA polymerases, which enable the replicase to circumvent these obstacles and complete chromosomal replication. Additional processes involving DNA polymerases are brought into action during heightened levels of DNA damage. We review here DNA polymerase structure, catalytic mechanism, and several pathways in which various bacterial DNA polymerases act.
Calcium Signaling
Authors: Brini Marisa , Fedrizzi Laura , Carafoli Ernesto
Published: February 2008

Calcium is a universal second messenger that controls many cellular reactions. Considering its pleiotropic role, it seems evident that the cells, to get a specific message in the proper time and manner, need precise and efficient mechanisms to encode and decode Ca2+signals. Generally, extracellular stimuli are converted in a transient increase in cytosolic Ca2+concentration, [Ca2+]c, which, in turn, modulates cell function. In the last two decades, improvements in the development of probes and instrumentation for Ca2+imaging have led to the discovery that the coordinated action of different players is responsible for a complex spatio‐temporal organization of the Ca2+signal. It is intriguing to observe that cells can encode and discriminate Ca2+signals not only according to their magnitude but also according to their localization (microdomains) and shape; i.e., cells can discriminate between sustained and oscillatory signals. Even more, in the case of oscillations, messages can be read differently according to the frequency of the oscillatory signals. The mechanisms by which cells decode Ca2+signals are now explored in numerous laboratories. This article focuses on the autoregulation properties of the Ca2+signals. It will show that Ca2+itself is central in the regulation of the Ca2+signal. It will also show that it can act as a first and second messenger and that it can modulate the activity and the availability of the other players in the signaling operation.
Catalytic Antibodies (Abzymes), Synthetic
Authors: Brogan Andrew P. , Dickerson Tobin J. , Janda Kim D.
Published: February 2008

Catalytic antibodies have emerged as powerful tools for the chemical biologist, enabling the design and realization of specific catalysis for a wide range of chemical reactions. Catalytic antibodies are grounded upon transition state theory and envisioned as programmable mimics of enzyme catalysis. Affinity maturation of the immune response for a small‐molecule hapten elicits binding site complementarity within an antibody that facilitates chemical catalysis. The evolution of hapten design strategies for chemical catalysis is presented, including the transition state analog approach, strain‐induced hapten design, “bait‐and‐switch,” and “reactive immunization.” The range and scope of antibody catalysis is examined by reaction class, highlighting structural and mechanistic investigations to explore the roots of chemical catalysis by these designer biocatalysts. Recently, antibodies, regardless of disposition or origin, have been shown to catalyze the oxidation of water, equipping the antibody with a mechanism for antigen decomposition. These recent developments are presented along with the utilization of this pathway in the oxidative degradation of a commonly abused drug. The achievements in antibody catalysis have enriched our scientific understanding of chemical catalysis, particularly by biological molecules in aqueous systems. However, realizing more operative rate enhancements on the same order as natural enzymes remains as the “holy grail” of this field.
Cell Membrane Dynamics
Authors: Kenworthy Anne K.
Published: February 2008

Cell membranes are two‐dimensional fluids that exhibit a wide range of dynamic behaviors. Recent technical advances have enabled unprecedented views of membrane dynamics in living cells. In this technical review, we provide a brief overview of three well‐studied examples of membrane dynamics: lateral diffusion of proteins and lipids in the plane of the membrane, vesicular trafficking between intracellular compartments, and exchange of proteins on and off membranes. We then discuss experimental approaches to monitor membrane protein and lipid dynamics, and we place a special emphasis on the use of genetically encoded fluorescent probes and live cell‐imaging techniques.
Chemical Libraries: Screening for Biologically Active Small Molecules
Authors: Schuffenhauer Ansgar
Published: February 2008

The screening of chemical libraries is one of the major sources for new leads in drug discovery. The large size of chemistry space compared with the library sizes that are feasible to screen requires careful selection of the compounds for the screening library to maximize screening success. Besides issues around technology compatibility and chemical tractability of the compounds, the main objective is to increase the probability of obtaining hits for the screened targets. Diversity selection approaches have often shown only limited success. In the absence of any knowledge, it is proposed to screen smaller “lead‐like” ligands with preference. When knowledge about the target is available, it can be used for target‐focused compound selection or for library design. In the screening process, physical high‐throughput screening (HTS) can be combined with virtual screening either to avoid the high‐throughput primary screen of the whole library or to limit false negatives by combining primary HTS and virtual screening results. Screening an initial subset then using the results obtained to predict likely hits for subsequent screening rounds in sequential screening can lessen the number of compounds to be screened, but it causes a greater logistics effort and has the risk of missing compounds that are not well represented structurally by the initial set. Data analysis and visualization of the screening results are a necessary final step of a screening campaign to ensure that the prioritization of compounds followed up is based on all available relevant information.
Collagen Triple Helix: Stability
Authors: Bächinger Hans Peter , Mizuno Kazunori
Published: February 2008

Collagens are the most abundant extracellular matrix proteins in multicellular animals. They all contain a name‐giving collagen triple helix, which connects their three chains and varying amounts of other noncollagenous protein domains. To form the triple helix a repeated sequence of ‐Gly‐Xaa‐Yaa‐ is required, where Xaa and Yaa can be any residue. Each chain forms a polyproline‐II like left‐handed helix. The three chains are staggered by one residue from each other, and form a right‐handed helix. Twenty eight types of collagen molecules have been identified in mammals. The stability of the collagen triple helix is based on the length and the amino acid sequence of each polypeptide chain, and also by the presence of interchain cross‐links and/or trimerization domains. The 4(R)‐hydroxylation of proline residues in the Yaa position significantly increases the stability of the collagen triple helix.
Cyclooxygenase Inhibition Mechanisms: Recent Advances
Authors: Turman Melissa V. , Blobaum Anna L. , Konkle Mary E. , Marnett Lawrence J. , Hancock A.B.
Published: February 2008

Cyclooxygenases (COXs) are key enzymes of bioactive lipid metabolism that catalyze the committed step in prostaglandin biosynthesis. Inhibition of COX catalysis is a principal mode of action of nonsteroidal antiinflammatory drugs (NSAIDs). The combination of structural and functional analysis of COX‐inhibitor interactions has provided important insights into the molecular determinants of inhibition. Although COX protein structure does not change significantly on inhibitor binding, a surprising variety of binding modes and molecular interactions are observed with different NSAIDs. This article focuses on recent advances in our understanding of these interactions with emphasis on arylcarboxylic acid‐based inhibitors and their derivatives.
Cytochrome P450 Monooxygenases, Chemistry of
Authors: Denisov Ilia G
Published: February 2008

Cytochromes P450 monooxygenases represent a large superfamily of heme enzymes, which require a dioxygen molecule and two electrons supplied by a NAD(P)H‐dependent protein redox partner to form catalytically active high‐valent ferryl‐oxo intermediate. These heme enzymes are found in most organisms from all biological kingdoms and catalyze various oxidative chemical transformations important for the biosynthesis of steroid hormones, vitamins, signaling molecules, and many other compounds, as well as for the metabolism of xenobiotics.
Small Molecule Inhibitors: Design and Selection
Authors: Che Jianwei , Liu, Yi , Gray Nathanael S.
Published: February 2008

The discovery and optimization of small‐molecule inhibitors for the treatment of human disease has been the major focus of the pharmaceutical industry for more than a century. In the last decade, they have also attracted increased attention from academia because they provide a powerful means to interrogate biologic systems in an acute fashion. Although pharmaceutical companies have identified many small‐molecule inhibitors for drug targets, to find a desirable small‐molecule inhibitor for a specific target is still a major challenge for drug discovery and for chemical biology. Here, we present an overview of the computational approaches that can be exploited to discover small‐molecule inhibitors for protein targets of interest.
Directed Evolution: Novel and Improved Enzymes
Authors: Wen Fei , McLachlan Michael , Zhao Huimin
Published: February 2008

By mimicking Darwinian evolution in the test tube, directed evolution has become a powerful tool for engineering novel enzymes for basic and applied biology research and medicine. Unlike structure‐based rational design, directed evolution is capable of altering single or multiple functional properties such as activity, specificity, selectivity, stability, and solubility of naturally occurring enzymes in the absence of detailed knowledge of enzyme structure, function, or mechanism. More recently, directed evolution has also been used to engineer metabolic pathways, viruses, and whole microorganisms, and to address fundamental problems in biology. The success of directed evolution has been largely fueled by the development of numerous molecular biology techniques that enable the creation of genetic diversity through random mutagenesis or homologous or nonhomologous recombination in the target genes and the development of powerful high throughput screening or selection methods as well as by novel applications. This review will highlight the key developments in directed evolution and focus on the design and engineering of novel enzymes through directed evolution and their implications in chemical biology.
DNA
Damage: Sensing
Authors: Yang Xiaohong H. , Zou Lee
Published: February 2008

Maintenance of genomic stability is essential for the survival of cells, organisms, and species. Genomic stability relies on the complete and accurate transmission of genetic materials from mother cells to daughter cells and from one generation to the next. This task is daunting, however, because the genome is constantly challenged by numerous intrinsic and extrinsic stresses that damage deoxyribonucleic acid (DNA). If left untreated, such damage can destabilize the genome by introducing gene mutations, duplications, and chromosomal rearrangements such as deletions and inversions, which fortunately does not normally happen as cells evolve a complex damage sensing and signaling mechanism named the DNA damage and replication checkpoint. Checkpoint activation effectively pauses the progression of the cell cycle, allowing more time for the removal of DNA lesion. Moreover, activated checkpoint also regulates and coordinates a number of cellular processes including DNA repair, DNA replication, and chromatin remodeling to alleviate the stress on the genome. At the core of the checkpoint‐signaling network, a family of phosphoinositide‐3‐kinase (PI‐3K)‐like kinases and their regulatory partners serve as both DNA damage sensors and initiators of checkpoint signaling. In this article, we will discuss in detail how DNA damage is sensed and processed by the DNA damage and replication checkpoint. We will also discuss how signals generated at sites of DNA damage are propagated and relayed through the checkpoint pathways to influence other cellular events.
Drug Transport in Living Systems
Authors: Elbaz Yael , Schuldiner Shimon
Published: February 2008

Living organisms are constantly assailed by a host of harmful chemicals from the environment. Because of the diversity of these “xenobiotics”, cellular survival mechanisms must deal with an immense variety of molecules. Polyspecific drug transporters supply one such strategy. They recognize a wide range of dissimilar substrates that may differ in structure, size, or electrical charge, and they actively remove them from the cytoplasm. As such, these transporters provide an essential survival strategy for the organism. However, given that the substrates of these multispecific transporters include many antibiotics as well as antifungal and anticancer drugs, they are associated with the phenomenon of multidrug resistance (MDR) that poses serious problems in the treatment of cancers and infectious diseases, and some of them are coined multidrug transporters (MDTs). As expected from their central role in survival, these transporters are ubiquitous, and in many genomes, several genes coding for putative MDTs have been identified. MDTs are found in evolutionary unrelated membrane transport protein families, which suggests that they might have developed independently several times during the course of evolution. In this review, we discuss some basic concepts regarding drug transport from bacteria to humans.
Endoplasmic Reticulum
Authors: Bánhegyi Gábor , Benedetti Angelo , Csala Miklós
Published: February 2008

Several pathways are compartmentalized in the endoplasmic reticulum (ER). These intraluminal activities require the passage of substrates, cofactors, and products through the ER membrane. The arguments for a general permeability of the ER membrane are contradicted by strong biochemical, pharmacological, clinical, and genetic evidence, which indicates that the lipid bilayer has a barrier function and that specific transport activities are needed in the membrane. Consequently, the ER lumen can be regarded as a separate metabolic compartment. This article overviews the best characterized intraluminal processes in which the compartmentation is important either by defining an intraluminal milieu, by limiting the rate of the reaction, by determining the specificity, or by creating a common substrate pool because of the colocalization.