2006

ZOOLOGY

1.) Year: 2006 I Volume: 2 I Issue: 2 I Page No.: 136-149 DOI: 10.3923Mzr.2006.136.149

The Relation between Biological Consequences and Temperature on Some Non-Mammalian

Species

R.G. Ahmed

Abstract: The number of reports on the effects of temperature is still increasing because of the
temperature is one of the most encountered stressful factors in the environment, thus it deemed
important to survey the literatures for effects of temperature on the biological consequences. The
objective of this review was to establish the thermoregulatory response and adaptation of some
non-mammalian species during temperature. Although, there was relative scarcity of information
on the relation between oxidative stress and antioxidant enzymes during temperature, this review
great interest to elicit this relation in non-mammalian species. Here, this review suggests that, the
increase in the oxidative stress due to temperature may be a reason for such decrease and
exhaustion of antioxidant enzymes and a sequence of cellular injury or death, because of
increased endogenous production of the free radicals. However, there was exception in this
hypothesis because this argument is still ambiguous because of the difficulties of the direct
observation of the active oxygen species in the biological systems due to their short lifetime.
Taken together, because of one of the most important functions of heat shock protein is to protect
the organisms from the deleterious effects of temperature, thus, it can be hypothesized that the
formation of heat shock protein and antioxidant enzymes may be related to the changes in the
levels of free radicals in non-mammalian species during temperature.

2.) Year: 2006 I Volume: 2 I Issue: 2 I Page No.: 123-128 DOI: 10.3923Mzr.2006.123.128

Nutritive Evaluation of Edible Trash Fish. HI: Medicinal and Commercial Use of Lipids of Trash
Fish

Rukhsana Talat, Rafia Azmat , Talat Syeda and Yasmeen Akhter

Abstract: The trash fish has great economic importance with reference to lipids. The total lipids
was extracted by soxhelet extraction method and is further analyzed for cholesterol phospholipid
and glyceride. Recent research shows the utilization of lipids (fatty acids) obtained from trash in
different medicinal and commercial purposes. Results were explained in relation with utilization
of trash fish oil, which caught during fishing. It was observed that lipids contain vitamin A. C D
and E which depend upon the fish species. Fatty acids from the fish also used in manufacturing
of soap, fungicides and insecticides. Pharmaceuticals for coronary diseases and heat resistant
paints. This investigation may be beneficial in utilization of trash.
 3.) Year: 2006 I Volume: 2 I Issue: 2 I Page No.: 110-115 DOI: 10.3923/15zr.2006.110.115

Nutritive Evaluation of Edible Trash Fish: II Use of Trash Protein in Cereal Food Diet

Rukhsana Talat and Rafia Azniat

Abstract: The essential and non essential amino acid has been estimated to determine the quality
of protein of ediable fishes from trash fish collected from Karachi fish harbor. The crude protein
was analyzed by standard method. The amino acid contents from protein hydrolyze were
analyzed by high speed amino acid analyzer model 835. The results were discussed in order to
evaluate the protein value of the ediable species present in trash and its utilization as a food of
poultry, supplement of cereal food because of nutritional point of view, man cannot survive on a
bread diet alone. It was suggested that the variations in values of protein contents of edible fishes
of trash may be due to difference in species, size, age, physiological state, time and region of
catch.

4.) Year: 2006 I Volume: 2 I Issue: 2 I Page No.: 100-109 DOI: 10.3923Thzr.2006.100.109

Paleobiogeography of the Siwalik Ruminants

Muhammad Akbar Khan and Muhammad Umer Farooq

Abstract: During the Miocene, the Indian plates moved closer to Eurasia causing the further
elevation of the Alps, Himalayas and other mountain belts. The Neogene terrestrial rocks
generally the Siwaliks, form the Sub-Himalayas. Early pecarons in Africa, Pakistan and India are
poorly known. Ruminant fossils are numerous in the Siwaliks. The cervoid are found in Eurasia
and presumably evolved there but some fragmentary fossils are found in Bugti hills and two
specimens are collected from the Chinji Formation. Tragulids are found in the Lower Miocene of
Egypt, East Africa and Nambia and Giraffoids evolved in Africa. The Bovid (Eotragus) appeared
in Europe and the same time in the lower Siwalik of Pakistan. Changes in global climate had a
direct impact on the distribution of species. The global climate also permitted Asian animals to
disperse into Europe. Faunal exchange between Europe and the Siwaliks occurred through SE
Europe and Anatolia. While extensive landmasses were slowly being formed out of a number of
smaller fragments, sea level changes connected and disconnected these areas and allowed for,
or inhibited faunal exchange. The effects of the sea level changes were strongest during the Early
Miocene, whereas from the Middle Miocene onward, the land sea distribution seems to have been
less affected and less important in controlling the geographical distribution of mammals.

5.) Year: 2006 I Volume: 2 I Issue: 1 I Page No.: 91-99 DOI: 10.3923/' zr 2006 91 99

First Record on Larval Development of the Cirripedian Parasite Loxothy/acus texanus (Cirripedia-
Rhizocephala) Under Laboratory Conditions in Mexico

H. Vazquez-Lopez , F. Alvarez-Noguera and 1. Franco-Lopez

Abstract: Crabs with mature parasites were put on individual aquariums of 20 L of capacity and
with an initial salinity of 100/00. Salinity was gradually increased 1%0 until it reached a point in
which parasites expeled their eggs or larvae. Larvae at different developmental stages obtained
from each sample were preserved in 70 and ethanol to be studied afterwards. From 20 crabs
employed, only 14 of them produced eggs and other 6 died after a few days at the aquariums.
The mature externas expelled from 8000 to 160000 clustered eggs. After 24 h from the beginning
of cellular division, larvae hatch. This larvae are called nauplius 1. This stage lasted 24 h, after
which all larvae entered an excitation period, where they rapidly moved, to then pass a new molt
process resulting in a new larval stage, nauplius 2. Elevating salinity a unity, externas started to
expel eggs, nauplis larvae 1 hatched from them, but they only survived less than 24 h. As salinity
increased, nauplius larvae lived longer, even to realized a molt. At a 15 Woo salinity, larvae
reached cypris stage with no problem, but with a salinity higher than 25 Woo, larvae died after a
few hours of hatching. We can conclude that: the rhizocephalan Loxothy/acus texanus has two
nauplius stages, the nauplius and cypris larvae presented similar morphological characteristics to
related species of rhizocephalans and a salinity interval from 15 to 20%o report the same result.

6.) Year: 2006 I Volume: 2 I Issue: 1 I Page No.: 84-90 DOI: 10.3923/i zr 2006 84 90

Nesting Habitats and Nesting Success of Hill Mynahs Gracile religion in Thailand

Manee Archawaranon

Abstract: Nesting habitats of Hill Mynah Gracula religiosa were studied in order to gain a
perspective of habitat features which were favoured by natural selection. A total of 76 nest trees
and 310 neighbour trees of northern Hill Mynah (G. r. intermedia) and 25 nest trees and 136
neighbour trees of southern Hill Mynah (G. r. religiosa) were studied in eight provinces of Thailand
between 6° and 20°N from 1991 to 1999. Nest characteristics including nest height, nest size,
nest depth, cavity entrance, angle of nest cavity and cavity entrance were recorded. The
characters of nest trees, including condition types, the height, canopy and trunk were studied.
Habitat characteristics were measured within a square plot of 20x20 m around nest trees. Number
and the characters of neighbour trees around each nest tree, distance from nest trees to the
nearest neighbour trees were recorded. The results showed that Hill Mynah nest trees were taller,
bigger and had thicker canopies than their neighbour trees. Their nests were higher and farther
from the tree boles in dense canopies. Nest trees were live and solitary in the areas with foliage
cover. Habitats of successful nests were different from unsuccessful ones in the term of higher
first branches, bigger canopies, more surrounding trees and farther from neighbour trees.
Although the natural selection successfully shapes the form of Hill Mynah nesting habitats to avoid
natural predators and unfavourable climates, heavy human interference is the major cause of
nesting failure in this species.

7.) Year: 2006 I Volume: 2 I Issue: I I Page No.: 73-76 DOI: 10.3923/i r 2006 73 76

The Seasonal Effects of Linda intestinalis L. (Cestodes: Pseudophllidae) on Alburnus album us

(Cyprinidae)
Mustafa Koyun

Abstract: In this study seasonal effect of Ligu/a intestinalis of plerocercoids in Alburnus alburnus
(bleak) have been investigated. Out of 244 A. alburnus examined and 40 specimens were found
to be heavily infected with parasites mentioned above (16%). The highest infection rate has been
found in July and August (36 and 44%). In this study among the all fish species A. alburnus was
only infected fish by this parasite in Enne Darn Lake. According to ages and seasonally the ratio
of infection were calculated.

8.) Year: 2006 I Volume: 2 I Issue: 1 I Page No.: 60-72 DOI: 10.3923/i zr 2006 60 72

Ultrastructure of Sperm Head Differentiation in the Lizard, Acanthodadylus boskinus (Squamata,

Reptilia)

O.A. Al-Dokhi

Abstract: The aim of the present study was to describe the sperm head differentiation in the lizard
Acanthodacty/us boskinus at the ultrastructural level. For this purpose, five adult male lizards
were collected during April and May, 2004 from the desert at the north-east area of Riyadh city,
Saudi Arabia. Testes of the lizards were processed for transmission electron microscopy.
Thorough observation of the ultrastructural differentiation events of the sperm head has led to a
concept of four sequential morphogenetic phases; Golgi phase, cap phase, nuclear elongation
and chromatin condensation phase and maturation phase. The Golgi phase is initiated by the
proliferation of Golgi complexes in the early spermatids to generate numerous microvesicles and
the phase is terminated by the formation of a voluminous acrosomal vesicle. Flattening of the
developed acrosomal vesicle over the anterior nuclear portion to form a cap associated with
dissolution of the acrosomal granule are the features of the cap phase. Subsequent elongation of
the spermatid nucleus accompanied with nuclear chromatin condensation are the features of the
following phase. The final maturation phase is characterized by complete chromatin condensation
and disappearance of the microtubule manchette. The general features of the differentiation
process, which accord with the common criteria of other reptiles, as well as the existing
differences are discussed.

9.) Year: 2006 I Volume: 2 I Issue: 1 I Page No.: 48-59 DOI: 10.3923/ zr.2006.48.59

The Relation between Biological Consequences and High Temperature in Mammals

R.G. Ahmed

Abstract: Because of the temperature is one of the most encountered stressful factors in the
environment, it was deemed important to survey the literature for reports on high temperatures or
hyperthermia exposure durations at which biological effects occur. Since that time, several
method of heating the entire body have evolved, including the artificial induction of fever, the
wrapping of an anesthetized patient in plastic and dipping them in hot wax and heating the blood
supply. The aim of this review was to determine the changes in tissue temperature and the
duration of this effect. In general, the higher the temperature or the longer the hyperthermia, the
greater the chance for observing a perturbation to the biological effects. It appears reasonably
well established that, short exposure to sharply-elevated temperatures result in a protective effect
against further thermal insult; the generation of heat shock proteins by cells coincides with the
onset of such "thermal protection". It can be concluded that, thermal damage increases as the
time at an elevated temperature increases.

10.) Year: 2006 I Volume: 2 I Issue: 1 I Page No.: 34-47 DOI: 10.3923/ zr.2006.34.47

Morphologic and Morphometric Analysis and Growth Rings Identification of Otoliths: Sagitta,
Asteriscus and Lapillus of Caranx caballus (Pisces: Carangidae) in the Coast of Colima, Mexico

M. Gallardo-Cabello , E. Espino-Barr , A. Garcia-Boa , E.G. Cabral-Solis and M. Puente-Gomez

Abstract: This study is a description and morphometric analysis of the otoliths sagittae, asterisci
and lapilli of the green jack Caranx caballus (Gunther, 1869) in the tropical Mexican Pacific. The
relationship among length, width and weight of the sagittae is expressed by the following
equations: y = 0.9350.832 (rostrum-antirostrum), y = 0.272x1.139 (rostrum-width) andy =
0.00007x2.524 (rostrum-weight). In the case of the asterisci: y = 1.6230.81 (length-width) and y
= 0.0005x1-657 (length-weight). For the lapilli y = 1.0610-874 (length-width) and y = 0.0003x2.796
(length-weight). The growth of these otoliths was also related to the length of the fish. The average
length was calculated for each of the four growth rings identified in the sagittae and the asterisci;
the results are: 1 = 16.82 cm, 2 = 27.78 cm, 3 = 34.66 cm and 4 = 40.27 cm.

11.) Year: 2006 I Volume: 2 I Issue: 1 I Page No.: 30-33 DO I: 10.3923/0zr.2006.30.33

Biology and Feeding Potential of Coccinella septumpunctata on Mustard Aphid, Lipaphis etysimi

Rizwana Khursheed , Barkat Hussain , S.B. Ahmad and M. Ashraf

Abstract: Different developmental stages of Coccinella septumpunctata was observed that the
egg, larval, pre-pupal and adult stages occupied more duration in first generation as compared to
second, total larval period 16±1.73 days and pupal period, 7.5±0.87 days was more in first
generation in contrast to second 13.5±0.87 days and 6.5±0.87 days, respectively. However,
similar was the trend with respect to longevity of males and females.Adult stage of Coccinella
septumpunctata consumed more aphids in both generations as compared to larval. Nevertheless,
when a comparison was made, between larval instars, it was observed that older larvae consume
more number of aphids/day than younger ones.

12.) Year: 2006 I Volume: 2 I Issue: 1 I Page No.: 30-33 DO I: 10.3923/0zr.2006.30.33

The Camel Tick, Hyalomma (Hyalomma)dromedard Koch, 1844 (Ixodoidea: Ixodidae):

Description of the Egg and Redescription of the Larva by Scanning Electron Microscopy
Ashraf Ahmed Montasser

Abstract: The present study describes the egg of Hyalomma (H.) dromedarii for the first time and
adds more features to the larva using Scanning Electron Microscopy (SEM) in order to extend our
knowledge on these acarine stages to be useful for further taxonomical or control studies. With
the purpose of presenting exact description of acarine eggs, it is preferable to examine them both
with and without SEM processing. SEM processing caused partial removal of the chorion which
makes the egg shell clear and easily observed. The study revealed rough surface of egg shell
which was surrounded by the chorion. The egg shell was perforated particularly at poles. The
chorion appeared as a finely perforated cloth. Different forms of bumps were noticed between
egg shell and chorion. Length, width, 11w ratio and pore diameter of the egg were measured.
SEM investigation of the larva revealed smooth scutum with slight irregular ornamentation and
horizontally folded extensible cuticle with vertical ridges. At least 2 types of cuticular openings
were noticed on the extensible cuticle of the idiosoma. The first type was represented by 1 pair
on dorsal side and 2 pairs on ventral one. It was surrounded with thick integumental ring and
guarded with 2 internal lips. The second type was numerous, slit-like and without rings or lips.
Dorsolateral plate of the hypostome carried numerous oval, tile-like and elevated denticles while
ventral one carried 4 rows of posteriorly directed retrograde conical denticles. Mouth enclosed 2
cheliceral digits, each terminated with 3 lobes. Each lobe is supported with 2 or 3 conical denticles
which were externally directed to the posterior. Haller's organ on the tarsus of the first pair of legs
consisted of anterior pit and posterior capsule. The pit contained 6 conical sensillae while the
capsule opening had extensively branched margin. Measurements of the whole body, idiosoma,
scutum, eye, capitulum, hypostome, palp, cuticular pores, legs and Haller's organ sensillae of the
larva are also presented.

13.) Year: 2006 I Volume: 2 I Issue: 1 I Page No.: 1-13 DOI: 10.3923/i zr 2006 1 13

The Spiny Rat Mite Echino/aelaps echidninus (Berlese, 1887) (Dermanyssoidea: Laelapidae):
Redescription of the Female with Emphasis on its Gnathosoma, Sense Organs, Peritreme and
Pulvilli

Ashraf Ahmed Hontasser

Abstract: The present Scanning Electron Microscopic (SEM) study includes redescription of
female Echinolaelaps echidninus with emphasis on its gnathosoma, sense organs, peritreme and
pulvilli which were rarely described in superfamily Dermanyssoidea. Chaetotaxy of dorsal shield
revealed 40 pairs of setae, 22 on prosoma and 18 on opisthosoma. Epigynial plate carried 5 pairs
of setae. Gnathosoma consisted of long basis capituli carrying median hypostome and 2 lateral
pedipalps. Hypostome had dorsal labrum covered with finger-like processes, 2 lateral 3-
segmented chelicerae and ventral labium carrying 4 lobulated plates. Function of labrum
processes might be chemosensory while labium lobules might be mechanical, preventing solid
material from entering the oral cavity. Palpal and foreleg tarsal organs comprised 10 and 16
sensillae, respectively. Sensillae of palpal organ were mostly chemoreceptors while those of
tarsal organ were probably mechanoreceptors. Peritremal pit contained 4 rows of hand-like
papillae and 5 concentric rows of minute papillae. Each pulvillus terminated with 2 medioventral
claws. Pulvillus I had terminal integumental folds while each pulvillus II-IV had 2 lateral comb-like
plates. Each plate carried 8-10 processes.

14.) Year: 2006 I Volume: 2 I Issue: 2 I Page No.: 192-203 DOI:

10.3923Thzr.2006.192.203

Toxic Effects of Two Insecticides on Brown Plant Hopper, Nilaparvata lugens and its Predators
Micraspis discolor and Lycosa pseudoannulata

T.K. Biswas, M.A. Rahman , M.M.H. Khan , M.M. Alam and M. lahan

Abstract: The experiment was conducted in the net house and laboratory to
determine the effectiveness of two insecticides viz., Cymbush (Cypermethrin) and Brifer
(Carbofuran) on brown plant hopper, Nilaparvata lugens and the toxic action of these
insecticides to the predators lady bird beetle, Micraspis discolor and wolf spider, Lycosa
pseudoannulata. Effectiveness of the insecticides was assessed on the basis of percentage
of corrected mortality of brown plant hopper, lady bird beetle and wolf spider under
laboratory condition at 24, 48 and 72 h after treatment. Cymbush 10EC @ 0.05 kg a.i. ha -
1
. caused 100% mortality of insect populations at different time intervals. All the doses of
Brifer
5G caused a good mortality of N lugens at different time intervals and was effective at
higher dose. Cymbush 10EC @ 0.04 kg a. i. ha-1. and Brifer 5G © 0.5 kg a.i. ha -1. were
found very effective against N. lugens. The effectiveness of Cymbush 10EC decreased and
Brifer SG increased with increasing time interval. Cymbush 10EC @ 0.05 kg a.i. ha -1. was
highly toxic and 0.01 kg a.i. ha -1 . was less toxic to both the predators. Brifer 5G © 0.5 kg
a.i. ha -1 . was least toxic to the predators. Between the two predators L. pseudoannulata
was more susceptible to the insecticides than H. discolor.

COCLUSION
Research and thesis papers about Zoology from 2006 was more about mammals. They
focused on the Biological Consequences of the high temperature in both non-mammals and
mammals, nutritive evaluation, new discovered habitats and how the surroundings affect their
living.
GENETICS
1.) Production and metabolism of indole acetic acid in roots and root nodules of Phaseolus
mungo

By: Sisir Ghosh/DOI: 10.1016/S0944-5013(98)80037-2

The mature root nodules of Phaseolus mungo (L.), a leguminous pulse, contain higher amount of
indole acetic acid (IAA) than non-nodulated roots. The tryptophan pool present in the mature
nodule and young roots might serve as a precursor for the IAA production. Presence of IAA
metabolising enzymes - IAA oxidase and peroxidase - indicate the metabolism of IAA in the
nodules and roots. In culture, the symbiont, isolated from the nodules, produced a high amount
of IAA, when tryptophan was supplied in the medium as a precursor. The symbiont preferred l-
isomer over the dl- or d-isomer of tryptophan for IAA production. The important physiological
implication of the IAA production in the legume-Rhizobium symbiosis is discussed.

2.) The low level expression of chloramphenicol acetyltransferase (CAT) mRNA in

Escherichia coli is not dependent on either Shine-Dalgarno or the downstream boxes in
the CAT gene

By: Mariela Odjakova/DOI: 10.1016/S0944-5013(98)80037-2

Recent studies have shown that the canonical Shine-Dalgarno (SD)-anti-SD interaction is
dispensable for the initiation of translation of certain mRNAs in Escherichia coli. Alternative non-
SD sequences (located upstream from the initiation codon) and also downstream sequences
("downstream boxes") complementary to 16S rRNA were found to be involved in the initiation of
translation of mRNAs devoid of either SD or any leader sequences. In this study the
chloramphenicol acetyltransferase (CAT) gene was modified to remove the 5' terminal non-
translated region and/or the two potential downstream boxes in the CAT gene. Thus a series of
ten CAT gene constructs was created and expressed in E. coli under a strong constitutive
promoter. The results showed that CAT mRNAs devoid of both leader sequence nucleotides and
the two downstream boxes in the CAT gene remained active in vivo and produced CAT protein in
sufficient amounts for survival of the transformed cells at chloramphenicol concentrations up to
20-30 micrograms/ml.

3.) Genetic study of meat quality of a male border lines

By: L.G. Gaya (2006)

This research was conducted to estimate genetic and phenotypic parameters of meat quality,
performance,carcass and body composition traits in amale broiler line. Broilers studied belonged
to a sib testprogram, in which data from sibs of the individuals to be selected in this line, called
eliteflock, are collected. Performancetraits analyzedwere body weight at selection, body weight
at slaughter and ultrasound records of pectoral muscle. Carcass traits analyzed were breast meat
weight, eviscerated body weight and leg weight, and the body composition traits analyzed were
abdominal fat weight, liver weight and heart weight. Meat quality traits analyzed were initial pH,
pH at 6 h after slaughter, final pH, initial range of pH decline, final range ofpH decline,
lightness,redness, yellowness, weep losses, drip losses, shrink losses, and shear force.
(Co)variance components were estimated by the restricted maximum likelihood method, usingthe
MTDFREML software. The numerator relationship matrix was composed of 107,154 individuals.
For pH at 6 h after slaughte4 final pH and lightness, moderate heritability coefficients were
estimated; forthe other traits these coefficients were low Genetic correlation estimates obtained
indicated a small association between meat quality traits and performance, carcass andbody
composition traits, except for the selection to body weight atselection, which seemed to be able
to reduce water losses of meat. Genetic correlation estimates among meat quality traits could
orient the understanding of the mechanisms related to meat quality in the analyzed line; drip
losses, shear force and lightness seemed to be able to determine favorable correlated responses,
so their use was recommended as selection criteria if there was a need for improving meat quality
in the analyzed line. However this necessity was not apparent, since the genetic trends of meat
quality traits were small and favorable for meat quality in the broiler line analyzed.

4.) Biological considerations for a new approach to regulating genetically modified crops in
the United States

By: Ashley McDonough (2006) Oregon State University

Genetic engineering allows scientists to select genes from a variety of species, modify them, and
insert these genes into another organism. This endows an organism not only with a new segment
of DNA, but with a new trait, ability, or phenotype (Table 1). An additional benefit of this technology
is that it is very precise compared to traditional breeding, enabling single genes to be specifically
modified (Fernandez-Cornejo and Caswell 2006). This technology is often used for a variety of
purposes, such as using bacteria to produce pharmaceutical products, or to aid in basic genetic
research. Genetically engineered crops are subject to governmental regulation under three
agencies: the Environmental Protection Agency (EPA), the United States Department of
Agriculture (USDA), and the Food and Drug Administration (FDA), depending on the crop and the
type of modification.

5.) Comparative and Integrative genomic approach toward disease gene ident.
By: Annie Pei-Fen Chang/ DOI.10.17077/etd.v3b1w8k9 (2006)
The identification of disease genes (genes that when mutated cause human diseases) is an
important and challenging problem. Proper diagnosis, prevention, as well as care for patients
require an understanding of disease pathophysiology, which is best understood when the
underlying causative gene(s) or genetic element(s) are identified. While the availability of the
sequenced human genome helped to lead to the discovery of more than 1,900 disease genes,
the rate of disease gene discovery is still occurring at a slow pace. The use of genetic linkage
methods have successfully led to the identification of numerous disease genes. However, linkage
studies are ultimately restricted by available meioses (clinical samples) which result in numerous
candidate disease genes. This thesis addresses candidate gene prioritizations in disease gene
discovery as applied toward a genetically heterogeneous disease known as Bardet-Biedl
Syndrome (BBS). Specifically, the integration of various functional information and the
development of a novel comparative genomic approach (Computational Orthologous Prioritization
- COP) that led to the identification of BBS3 and BBS11. Functional data integration and
application of the COP method may be helpful toward the identification of other disease genes.
 6.) Isolation and characterization of high persistence mutants of Salmonel.

By: Andrew Richard Slattery/ DOI. 10.31274/rtd-180813-8316 (2006)

A small fraction of bacterial populations consist of "persistent" cells that are phenotypically distinct
from the majority of cells by their ability to avoid killing by a variety of antimicrobial challenges.
Persistence is distinct from resistance in that persistent cells are unable to grow in the presence
of the antimicrobial agent or treatment, but resume growth after the selection has been removed.
Presently, little is known about the genetic or physiological basis of persistence. In this study we
demonstrate that Salmonella enterica serovar Typhimurium (S. typhimurium) displays the
persistence phenotype. To better understand persistence in this important food-borne pathogen,
we have isolated 6 mutants that show an increased ability to survive exposure to a variety of
antibiotics without an increase in MIC values. All of the mutants isolated were found to have an
extended lag phase, but had wild type growth rates in exponential phase. Characterization of the
mutants indicates that multiple loci appear to contribute to persistence. Mapping the genes for the
high persistence phenotype will reveal new insights into this widely observed phenomenon.

7.) Genomic and population Genetic studies on THEILEIRA ANNULATA

By: William Weir/ University of Glasgow (2006)

Tropical theileriosis, caused by the tick-transmitted protozoan Theileria annulata, is a major

disease of cattle in many regions of the developing world. Current research is directed towards
developing a sub-unit vaccine, and it is therefore important that genetic diversity in field
populations of the parasite is investigated and quantified. The recently completed genome
sequence provided an opportunity to develop a panel of genetic markers for population studies
and also enabled the identification of novel antigen genes. The genome was bioinformatically
screened to identify micro- and mini-satellite loci, several of which were PCR amplified from a
series of diverse parasite stocks in order to characterise their polymorphism and to determine
their species-specificity. A panel of ten markers were selected for population genetic studies and
were used to genotype laboratorymaintained cell lines and clonal stocks of T. annulata isolated
from different countries. Cell lines comprised a multiplicity of genotypes, while clonal stocks
showed evidence of a single haploid genome. Preliminary population genetic analysis revealed a
large amount of genotypic diversity both between and within countries and indicated that the
parasite population is geographically sub-structured. Comparison of a limited number of stocks
isolated in different countries demonstrated that genetic differentiation between populations
positively correlates with intervening physical distance. A low standard index of association (I S
A) suggested that the population in Tunisia is in linkage equilibrium, indicating that the parasite
possesses a panmictic (randomly mating) population structure. To confirm these findings, a large
number of field isolates from Tunisia and Turkey were analysed (n = 305). This supported the
earlier finding that geographical sub-structuring separates panmictic populations and an almost
identical amount of genetic differentiation between countries was evident (FST = 0.05). Limited
linkage disequilibrium was observed in some populations and this was attributed to several factors
including inbreeding and the Wahlund effect, caused by putatively immigrant sub-populations. A
similar multiplicity of infection was demonstrated in vaccinated and unvaccinated animals and the
immunising genotype did not appear to establish in the field population. Multiplicity of infection
was instead shown to positively correlate with the host age in several sampling locations.

8.) Pine Martin CSI: Gaining from tongues and Faces

By: Tim Hofmeester (2006)

As a biology student, specializing in animal ecology, this thesis research was an ideal opportunity
to be able to gain more knowledge about genetics and the use of genetic techniques in the field
of animal ecology. I have learned a lot in this respect and I think I am now able to combine my
knowledge by designing genetic based methods to gain more insight into the ecology of animals.
At first, my report was only going to incorporate the part of my research on the Dutch pine marten
genetics, which is now Chapter 2. But as I have spent a lot of time in the lab, working on the non-
invasive genetics study, I decided to also add this part of my research to this report. The analysis
of Chapter 1 is however not very extensive, as I spend most of my time analysing the data for
Chapter 2. The working environment at Alterra gave me the opportunity to think about my ideas,
optimise my results and get the best out of my research. Therefore, I would like to thank Jan
Bovenschen, Hans Peter Koelewijn, Dennis Lammertsma, and Ivo Laros for helping me during
the study, both by discussing my ideas and helping me to get a grip on the ins and outs of working
in a molecular lab. Furthermore, I would like to thank my supervisors Fons Debets and Hugh
Jansman for supporting me during my research and making this thesis research possible.

9.) New Roles for Model Genetic Organisms in Understanding and Treating Human Disease:
Report From The 2006 Genetics Society of America Meeting
By: Allan Spradling (2006)

Fundamental biological knowledge and the technology to acquire it have been immeasurably
advanced by past efforts to understand and manipulate the genomes of model organisms. Has
the utility of bacteria, yeast, worms, flies, mice, plants, and other models now peaked and are
humans poised to become the model organism of the future? The Genetics Society of America
recently convened its 2006 meeting entitled “Genetic Analysis: Model Organisms to Human
Biology” to examine the future role of genetic research. (Because of time limitations, the meeting
was unable to cover the substantial contributions and future potential of research on model
prokaryotic organisms.) In fact, the potential of model-organism-based studies has grown
substantially in recent years. The genomics revolution has revealed an underlying unity between
the cells and tissues of eukaryotic organisms from yeast to humans. No uniquely human biological
mechanisms have yet come to light. This common evolutionary heritage makes it possible to use
genetically tractable organisms to model important aspects of human medical disorders such as
cancer, birth defects, neurological dysfunction, reproductive failure, malnutrition, and aging in
systems amenable to rapid and powerful experimentation. Applying model systems in this way
will allow us to identify common genes, proteins, and processes that underlie human medical
conditions. It will allow us to systematically decipher the gene–gene and gene–environment
interactions that influence complex multigenic disorders. Above all, disease models have the
potential to address a growing gap between our ability to collect human genetic data and to
productively interpret and apply it. If model organism research is supported with these goals in
mind, we can look forward to diagnosing and treating human disease using information from
multiple systems and to a medical science built on the unified history of life on earth.
 10.)Analysis of Repeat Induced Point (RIP) Mutations in Leptosphaeria maculans Indicates
Variability in the RIP Process Between Fungal Species

By: Angela P. Van (2006)

Gene duplication contributes to evolutionary potential, yet many duplications in a genome arise
from the activity of “selfish” genetic elements such as transposable elements. Fungi have a
number of mechanisms by which they limit the expansion of transposons, including Repeat
Induced Point mutation (RIP). RIP has been best characterized in the
Sordariomycete Neurospora crassa, wherein duplicated DNA regions are recognized after cell
fusion, but before nuclear fusion during the sexual cycle, and then mutated. While “signatures” of
RIP appear in the genome sequences of many fungi, the species most distant from N. crassa in
which the process has been experimentally demonstrated to occur is the
Dothideomycete Leptosphaeria maculans. In the current study, we show that similar to N. crassa,
nonlinked duplications can trigger RIP; however, the frequency of the generated RIP mutations is
extremely low in L maculans (< 0.1%) and requires a large duplication to initiate RIP, and that
multiple premeiotic mitoses are involved in the RIP process. However, a single sexual cycle leads
to the generation of progeny with unique haplotypes, despite progeny pairs being generated from
mitosis. We hypothesize that these different haplotypes may be the result of the deamination
process occurring post karyogamy, leading to unique mutations within each of the progeny pairs.
These findings indicate that the RIP process, while common to many fungi, differs between fungi
and that this impacts on the fate of duplicated DNA.

11.)Two Pif1 Family DNA Helicases Cooperate in Centromere Replication and Segregation
in Saccharomyces cerevisiae

By: Chi Fu Chen (2006)

Pif1 family helicases are found in virtually all eukaryotes. Saccharomyces cerevisiae (Sc)
encodes two Pif1 family helicases, ScPif1 and Rrm3. ScPif1 is multifunctional, required not only
for maintenance of mitochondrial DNA but also for multiple distinct nuclear functions. Rrm3 moves
with the replication fork and promotes movement of the fork through ∼1400 hard-to-replicate sites,
including centromeres. Here we show that ScPif1, like Rrm3, bound robustly to yeast centromeres
but only if the centromere was active. While Rrm3 binding to centromeres occurred in early to mid
S phase, about the same time as centromere replication, ScPif1 binding occurred later in the cell
cycle when replication of most centromeres is complete. However, the timing
of Rrm3 and ScPif1 centromere binding was altered by the absence of the other helicase, such
that Rrm3 centromere binding occurred later in pif1-m2 cells and ScPif1 centromere binding
occurred earlier in rrm3Δ cells. As shown previously, the modest pausing of replication forks at
centromeres seen in wild-type cells was increased in the absence of Rrm3. While a lack
of ScPif1 did not result in increased fork pausing at centromeres, pausing was even higher
in rrm3Δ pif1Δ cells than in rrm3Δ cells. Likewise, centromere function as monitored by the loss
rate of a centromere plasmid was increased in rrm3Δ but not pif1Δ cells, and was even higher
in rrm3Δ pif1Δ cells than in rrm3Δ cells. Thus, ScPif1promotes centromere replication and
segregation, but only in the absence of Rrm3. These data also hint at a potential post-S phase
function for ScPif1 at centromeres. These studies add to the growing list of ScPif1 functions that
promote chromosome stability.
 12.)MRG-1/MRG15 Is a Barrier for Germ Cell to Neuron Reprogramming in Caenorhabditis elegans

By: Martina Hadjuskova (2006)

Chromatin regulators play important roles in the safeguarding of cell identities by opposing the
induction of ectopic cell fates and, thereby, preventing forced conversion of cell identities by
reprogramming approaches. Our knowledge of chromatin regulators acting as reprogramming
barriers in living organisms needs improvement as most studies use tissue culture. We
used Caenorhabditis elegans as an in vivo gene discovery model and automated solid-phase
RNA interference screening, by which we identified 10 chromatin-regulating factors that protect
cells against ectopic fate induction. Specifically, the chromodomain protein MRG-1 safeguards
germ cells against conversion into neurons. MRG-1 is the ortholog of mammalian MRG15
(MORF-related gene on chromosome 15) and is required during germline development in C.
elegans. However, MRG-1’s function as a barrier for germ cell reprogramming has not been
revealed previously. Here, we further provide protein-protein and genome interactions of MRG-
1 to characterize its molecular functions. Conserved chromatin regulators may have similar
functions in higher organisms, and therefore, understanding cell fate protection in C. elegans may
also help to facilitate reprogramming of human cells.

13.)Distinct Roles for Peroxisomal Targeting Signal Receptors Pex5 and Pex7 in Drosophila

By: Francesca Di Cara (2006)

Peroxisomes are ubiquitous membrane-enclosed organelles involved in lipid processing and

reactive oxygen detoxification. Mutations in human peroxisome biogenesis genes (Peroxin, PEX,
or Pex) cause developmental disabilities and often early death. Pex5 and Pex7 are receptors that
recognize different peroxisomal targeting signals called PTS1 and PTS2, respectively, and traffic
proteins to the peroxisomal matrix. We characterized mutants of Drosophila melanogaster
Pex5 and Pex7 and found that adult animals are affected in lipid processing. Pex5 mutants
exhibited severe developmental defects in the embryonic nervous system and muscle, similar to
what is observed in humans with PEX5 mutations, while Pex7 fly mutants were weakly affected
in brain development, suggesting different roles for fly Pex7 and human PEX7. Of note, although
no PTS2-containing protein has been identified in Drosophila, Pex7 from Drosophila can function
as a bona fide PTS2 receptor because it can rescue targeting of the PTS2-containing protein
thiolase to peroxisomes in PEX7 mutant human fibroblasts.

14.)Conidial Morphogenesis and Septin-Mediated Plant Infection Require Smo1, a Ras GTPase-
Activating Protein in Magnaporthe oryzae

By: Michael Jay Kershaw (2006)

The pathogenic life cycle of the rice blast fungus Magnaporthe oryzae involves a series of
morphogenetic changes, essential for its ability to cause disease. The smo mutation was
identified > 25 years ago, and affects the shape and development of diverse cell types in M.
oryzae, including conidia, appressoria, and asci. All attempts to clone the SMO1 gene by map-
based cloning or complementation have failed over many years. Here, we report the identification
of SMO1 by a combination of bulk segregant analysis and comparative genome
analysis. SMO1 encodes a GTPase-activating protein, which regulates Ras signaling during
infection-related development. Targeted deletion of SMO1 results in abnormal, nonadherent
conidia, impaired in their production of spore tip mucilage. Smo1 mutants also develop smaller
appressoria, with a severely reduced capacity to infect rice plants. SMO1 is necessary for the
organization of microtubules and for septin-dependent remodeling of the F-actin cytoskeleton at
the appressorium pore. Smo1 physically interacts with components of the Ras2 signaling
complex, and a range of other signaling and cytoskeletal components, including the four core
septins. SMO1 is therefore necessary for the regulation of RAS activation required for conidial
morphogenesis and septin-mediated plant infection.

15.)Epidermal Remodeling in Caenorhabditis elegansDauers Requires the Nidogen Domain Protein

DEX-1

By: Kristen M. Flatt (2006)

Phenotypic plasticity is a critical component of an organism’s ability to thrive in a changing

environment. The free-living nematode Caenorhabditis elegans adapts to unfavorable
environmental conditions by pausing reproductive development and entering a stress-resistant
larval stage known as dauer. The transition into dauer is marked by vast morphological changes,
including remodeling of epidermis, neurons, and muscle. Although many of these dauer-specific
traits have been described, the molecular basis of dauer-specific remodeling is still poorly
understood. Here we show that the nidogen domain-containing protein DEX-1 facilitates stage-
specific tissue remodeling during dauer morphogenesis. DEX-1 was previously shown to regulate
sensory dendrite formation during embryogenesis. We find that DEX-1 is also required for proper
remodeling of the stem cell-like epidermal seam cells. dex-1 mutant dauers lack distinct lateral
cuticular alae during dauer and have increased sensitivity to sodium dodecyl sulfate. Furthermore,
we find that DEX-1 is required for proper dauer mobility. We show that DEX-1 is secreted from
the seam cells during dauer, but acts locally in a cell-autonomous manner. We find that dex-
1 expression during dauer is regulated through DAF-16/FOXO–mediated transcriptional
activation. Finally, we show that dex-1acts with a family of zona pellucida domain-encoding genes
to regulate dauer-specific epidermal remodeling. Taken together, our data indicate that DEX-1 is
an extracellular matrix component that plays a central role in C. elegans epidermal remodeling
during dauer.

CONCLUSION
Research and thesis papers about Genetics from 2006 focused more on how genetics
organisms can help us cure and prevent possible sickness that can affect our body. They
discovered new roles for Model Genetic Organisms in understanding and treating human
diseases.
MICROBIOLOGY
1.) Tumor Associated Microphages In a MaFIa Mouse Model

By; Adrian Brown Clifford (2006)- Brigham Young university

Recent evidence has shown the important role of macrophages in both tumor development and
progression. To investigate the role of macrophages we used a mouse model known as MaFIA
(Macrophage Fas Induced Apoptosis) mice that allows for the selective deletion of macrophages.
Mice were given melanoma cells at various stages of depletion. Tumor mass was measured and
organs were processed for flow cytometry to measure melanoma cell migration. The results show
that mice receiving depletion treatment have larger tumor sizes and weights than those mice
retaining their macrophage population. We detect metastasis in both the lung and kidney in both
macrophage depleted and non depleted mice. The more macrophages in an organ the larger the
amount of melanoma positive cells are detected

2.) Phylogenetics of North American Psoraleeae (Leguminosae): Rates and Dates in a

Recent, Rapid Radiation

By; Ashley N.Egan (2006)- Brigham Young University

The scientific discipline of phylogenetics involves understanding the diversity of life in the context
of history. Technological advances in molecular biology and computational power have created
an exponential increase in the number and kind of phylogenetic studies, allowing exploration of
all manner of questions concerning the evolutionary history of a group. This dissertation research
is focused on phylogenetic theory and applying these methods to the plant tribe Psoraleeae
(Leguminosae; Fabaceae) with an emphasis on North American (NAm) members. First, theory of
phylogeny estimation is explored in a review chapter focusing on strengths and weaknesses of
phylogenetic methodology. Second, methods are applied to estimating evolutionary relationships
within Psoraleeae based on six chloroplast (trnD/T, trnL/F, trnS/G, trnK, matK, and rpoB-trnC)
and two nuclear (ITS and waxy) DNA regions. This study explores approaches for coding
insertion-deletion events (gaps) as phylogenetic characters using maximum parsimony and
Bayesian Inference. Inclusion of gaps generally increased topological resolution and nodal
support, attesting to their phylogenetic utility. Findings suggest inclusion of gaps to be especially
useful in chloroplast-based studies as they represent a greater proportion of phylogenetic signal
as compared to nuclear regions. Past Psoraleeae classification schemes were tested and
taxonomic revisions suggested. Furthermore, phylogenetic comparative methods are used to
investigate correlation between geography and narrow endemism in NAm Psoraleeae.
Geographic variables of latitude, longitude, and elevation all correlate with range size and provide
support for Rapoport's rule of species-richness following latitudinal gradients. Finally, estimated
phylogenies are used to investigate divergence dates, nucleotide substitution rates, diversification
rates, and the impact of climate change, past and present, on diversification of NAm Psoraleeae.
Results suggest the group has undergone a recent, rapid radiation. Rates of molecular evolution
are fast, relative to other Legume lineages. Topological and temporal methods confirm the
existence of diversification rate shifts in NAm Psoraleeae. Quaternary climate oscillations are
shown to have significantly impacted diversification in the group while current shifts from mesic
to xeric climate regimes did not.
 3.) Characterization of the Role of SOX9 in CartilageSpecific Gene Regulation

By: Mary Ann Genzer (2006)- Brigham Young University

Although advances have been made toward understanding the complex mechanisms that
regulate the process of DNA transcription, the specific mechanisms of activation for many
individual genes remain unknown. In this study, we focus on the role the transcription factor SOX9
plays in activating cartilage-specific genes, specifically Col9a1 and Cartilage Link Protein
(CRTL1). Previously, enhancers of these genes containing single SOX9 binding sites were shown
to be activated through SOX9 binding. However, the hypothesis was made that in cartilage-
specific genes dimeric SOX9, as opposed to monomeric SOX9, is necessary for activation. We
identified a putative binding site adjacent to each of the known single SOX9 binding sites in the
Col9a1 D and E enhancers and in the CRTL1 enhancer. Electrophoretic Mobility Shift Assays
(EMSAs) were performed to determine whether SOX9 bound to these putative sites. Transient
transfections were then performed using wild-type and mutant enhancer- reporter plasmids to
determine whether these putative SOX9 binding sites were important for activation in vivo.
Although dimeric SOX9 bound to each of the enhancers in vitro, several different effects were
seen in vivo. In the presence of the wild-type Col9a1 D enhancer, no activation was seen.
However, when the enhancer was extended to include an additional pair of newly found SOX9
binding sites, expression was increased 10-fold. When any of the four SOX9 binding sites within
this enhancer were mutated, expression was completely eliminated, suggesting that
interdependent dimers or a tetramer of SOX9 is necessary for the activation of transcription. The
weaker Col9a1 enhancer E was found to increase gene expression minimally through binding of
either dimeric or monomeric SOX9. However, dimeric SOX9 was required for the activation of
gene expression by the CTRL1 enhancer. Through this study we validate the importance of not
just monomeric but of dimeric and possibly tetremeric SOX9 as an activator of cartilage-specific
gene expression.

4.) The Phylogeography of Prosopium in Western North America

By: Becky Akiko Miller (2006)- Brigham Young University

The mountain whitefish (Prosopium williamsoni) has been largely overlooked in population
genetic analyses despite its wide distribution in discrete drainage basins in western North America
for over four million years. Its closest sister taxa the Bear Lake whitefish (P. abyssicola),
Bonneville cisco (P. gemmifer), and Bonneville whitefish (P. spilonotus) are found only in Bear
Lake Idaho-Utah and were also included in the analyses. A total of 1,334 cytochrome b and 1,371
NADH dehydrogenase subunit 2 sequences from the Bonneville Basin, the Columbia River Sub-
basin, the lower Snake River Sub-basin, the upper Snake River Sub-basin, the Green River Basin,
the Lahontan Basin, and the Missouri Basin were examined to test for geographically based
genetic differentiation between drainage basins and sub-basins and phylogeographic
relationships to determine the invasion route of Prosopium into western North America and to aid
in understanding current relationships. Prosopium entered the region via the Missouri River
connection to Hudson Bay and moved in two waves: one colonized the lower Snake River Sub-
basin, Columbia River Sub-basin, and the Lahontan Basin; the second wave colonized the upper
Snake River Sub-basin, Bonneville Basin, Green River Basin, and established the Bear Lake
Prosopium. Mountain whitefish exhibit a large amount of geographical genetic differentiation
based on drainage basin except between the upper Snake River and the Bonneville Basin while
the Bear Lake Prosopium show large amounts of gene flow between the three species. The
apparent paraphyly of the mountain whitefish and the limited genetic structure of the Bear Lake
Prosopium warrant recognition in the management of Prosopium and raise questions regarding
species definitions in the group.

5.) Quorum Sensing in Dimorphic Fungi: Farnesol and Beyond

By: Kenneth W. Nickerson (2006)- University of Nebraska-Lincoln

Production of farnesol by Candida albicans is the first quorum- sensing system discovered in a
eukaryote (29). In C. albicans, accumulated farnesol affects both dimorphism (29, 50) and biofilm
formation (62). Fungal dimorphism is defined (64) as an environmentally controlled reversible
interconversion of morphology, particularly yeast and mycelial morphologies. Interest in this shift
derives from the dimorphic character of many fungi that are pathogenic toward plants and animals
(64). Numerous chemical and environmental parameters can shift the yeast-mycelium
dimorphism, including temperature, pH, glucose levels, nitrogen source, carbon dioxide levels,
transition metals, chelating agents, and inoculum size or initial cell density (64). Of these, the
inoculum size effect is probably the least well studied. For fungi such as Ceratocystis ulmi (28,
42) and C. albicans (29), cells develop as budding yeasts when inoculated at ≥106 cells per ml
and as mycelia when inoculated at (Table 1). In keeping with the precedent established by
homoserine lactone-based signaling in gram-negative bacteria (22), the inoculum size effect in
fungi is also called quorum sensing (29) and the extracellular cell density-dependent signals are
called quorumsensing molecules (QSMs). Thus, the chemical identity of the respective QSMs is
of interest. Apart from C. ulmi (28) and C. albicans (29), it is a “leap of faith” on our part that the
other cell density phenomena listed in Table 1 are mediated by QSMs.

6.) Pichia pastoris fermentation optimization: energy state and testing a growth-associated
model

By: Bradley A. Plantz (2006)- University of Nebraska-Lincoln

A growth-associated model was applied to the production of recombinant ovine interferon-τ

(rOvIFN-τ) with Pichia pastoris for the purpose of manufacturing pre clinical and clinical active
material. This model predicts that product yields will be the greatest when the specific growth of
the culture is maintained at a steady and optimal rate. However, rOvIFN-τ yields did not meet the
expected linear model but most closely corresponded to a polynomial relationship. After
transitioning from glycerol to methanol, product accumulated for 31–45 h, and then the yield
decreased. This production shift, which has been termed decoupling, was clearly related to time
on methanol and not culture density. It was determined that a correlation exists between the
decoupling point and a drop in energy state of the cell when expressing β-galactosidase. By
assigning decoupling as a constraint that limits productivity and by reformulating the growth
medium, the time prior to decoupling increased to 46.8 ± 2.4 h, product yield improved for rOvIFN-
τ from 203 to 337 mg l−1, and the coefficient of variation for yield decreased from 67.9 to 23.3%

7.) Isolation and identification of Streptomyces spp. from Venezuelan soils: Morphological
and biochemical studies. I.

By: Antoineta Tadei

The genus Streptomyces is represented in nature by the largest number of species and varieties
among the family Actinomycetaceae. They differ greatly in their morphology, physiology, and
biochemical activities, producing the majority of known antibiotics. The morphological and
biochemical characteristics of 71 Streptomycesspp. isolated from soil samples collected at
different places of Venezuela, are presented. A comparative analysis using the statistical software
Minitab shows that 67 of these isolates are presumably new strains, since they possess a very
low percentage of similarity with other reported species. Only four isolates shared 100% identity
with one, two or three reported Streptomyces spp.

8.) Neurologic Disease in Captive Lions (Panthera leo) with Low-Titer Lion Lentivirus Infection

By: Greg Brenan/ DOI: 10.1128/JCM.00577-06 (2006)

Lion lentivirus (LLV; also known as feline immunodeficiency virus of lion, Panthera leo [FIVPle])
is present in free-ranging and captive lion populations at a seroprevalence of up to 100%;
however, clinical signs are rarely reported. LLV displays up to 25% interclade sequence diversity,
suggesting that it has been in the lion population for some time and may be significantly host
adapted. Three captive lions diagnosed with LLV infection displayed lymphocyte subset
alterations and progressive behavioral, locomotor, and neuroanatomic abnormalities. No
evidence of infection with other potential neuropathogens was found. Antemortem
electrodiagnostics and radiologic imaging indicated a diagnosis consistent with lentiviral
neuropathy. PCR was used to determine a partial lentiviral genomic sequence and to quantify the
proviral burden in eight postmortem tissue specimens. Phylogenetic analysis demonstrated that
the virus was consistent with the LLV detected in other captive and free-ranging lions. Despite
progressive neurologic signs, the proviral load in tissues, including several regions of the brain,
was low; furthermore, gross and histopathologic changes in the brain were minimal. These
findings suggest that the symptoms in these animals resulted from nonspecific encephalopathy,
similar to human immunodeficiency virus, FIV, and simian immunodeficiency virus (SIV)
neuropathies, rather than a direct effect of active viral replication. The association of neuropathy
and lymphocyte subset alterations with chronic LLV infection suggests that long-term LLV
infection can have detrimental effects for the host, including death. This is similar to reports of
aged sootey mangabeys dying from diseases typically associated with end-stage SIV infection
and indicates areas for further research of lentiviral infections of seemingly adapted natural hosts,
including mechanisms of host control and viral adaptation.

9.) Identification of a Novel, Invasive, Not-Yet-Cultivated Treponema sp. in the Large Intestine of
Pigs by PCR Amplification of the 16S rRNA Gene

By: Lars Molbak/ DOI: 10.1128/JCM.01537-06 (2006)

Laser capture microdissection in combination with fluorescent in situ hybridization was used to
identify an unknown species of spirochetes from the pig colonic mucosa. The 16S rRNA gene
was PCR amplified, and the closest related type strain was Treponema bryantiiT (90.1%). The
spirochete, here named “Candidatus Treponema suis,” was associated with colitis, including
invasion of the surface epithelium as well as superficial parts of the mucosa.
Helical-shaped bacteria are commonly present in the gastrointestinal tract of animals and
humans. Intestinal spirochetes of pigs include several species of the genus Brachyspira, of
which Brachyspira hyodysenteriae and Brachyspira pilosicoli are important pathogens causing
swine dysentery, a severe mucohemorrhagic colitis, and spirochetal colitis, respectively (14, 15).
Culturing of Brachyspira as well as Treponema species is fastidious and not always successful.
Although ultrastructural differentiation is possible, the various spirochetes are quite similar
(typically 0.2 to 0.4 μm in width and 4 to 12 μm long) (11), and the size is not a useful criterion for
distinction in histopathological specimens. Alternative methods for species identification include
fluorescent in situ hybridization (FISH) with specific oligonucleotide probes targeting 16S or 23S
rRNA of the porcine pathogens B. hyodysenteriae and B. pilosicoli (2). Here, a novel technique,
laser capture microdissection (LCM)-FISH (7), was used to identify an unknown spirochete and
to establish its spatial distribution in the pig colonic tissue on archival tissue samples originating
from a study by Fossi et al. (4). The bacterial cells were visualized by FISH with a 16S rRNA-
targeting oligonucleotide probe, followed by laser capture microdissection (LCM) of the targeted
microcolony. The PCR was done directly on the captured cell material, and the dissected bacterial
cells were subsequently identified by analyses of the amplified 16S rRNA gene sequence.

10.) Presence of New mecA and mph(C) Variants Conferring Antibiotic Resistance
in Staphylococcus spp. Isolated from the Skin of Horses before and after Clinic Admission

By: Christina Schelmann/ DOI: 10.1128/JCM.00868-06 (2006)

Because of the frequency of multiple antibiotic resistance, Staphylococcus species often

represent a challenge in incisional infections of horses undergoing colic surgery. To investigate
the evolution of antibiotic resistance patterns before and after preventative peri- and postoperative
penicillin treatment, staphylococci were isolated from skin and wound samples at different times
during hospitalization. Most staphylococci were normal skin commensals and belonged to the
common coagulase-negative group. In some cases they turned out to be opportunistic pathogens
present in wound infections. MICs were determined for 12 antibiotics, and antibiotic resistance
genes were detected by microarray. At hospital admission, horses harbored staphylococci that
were susceptible to antibiotics or resistant to one group of drugs, mainly due to the presence of
new variants of the methicillin and macrolide resistance genes mecA and mph(C), respectively.
After 3 days, the percentage of Staphylococcus isolates displaying antibiotic resistance, as well
as the number of resistance genes per isolate, increased moderately in hospitalized horses
without surgery or penicillin treatment but dramatically in hospitalized horses after colic surgery
as well as penicillin treatment. Staphylococcus species displaying multiple resistance were found
to harbor mainly genes conferring resistance to β-lactams (mecA and blaZ), aminoglycosides
[str and aac(6′)-Ie-aph(2′)-Ia], and trimethoprim [dfr(A) and dfr(D)]. Additional genes conferring
resistance to macrolides [mph(C), erm(C), and erm(B)], tetracycline [tet(K) and tet(M)],
chloramphenicol [cat(pC221) and cat(pC223)], and streptothricin (sat4) appeared in several
strains. Hospitalization and preventive penicillin use were shown to act as selection agents for
multidrug-resistant commensal staphylococcal flora.

11.)Phylogenetic Analysis of “Candidatus Mycoplasma turicensis” Isolates from Pet Cats in the
United Kingdom, Australia, and South Africa, with Analysis of Risk Factors for Infection

By: Barbara Willi

Two hemotropic mycoplasmas have been recognized in cats, Mycoplasma haemofelis and
“Candidatus Mycoplasma haemominutum.” We recently described a third feline hemoplasma
species, designated “Candidatus Mycoplasma turicensis,” in a Swiss cat with hemolytic anemia.
This isolate induced anemia after experimental transmission to two specific-pathogen-free cats
and analysis of the 16S rRNA gene revealed its close relationship to rodent hemotropic
mycoplasmas. The agent was recently shown to be prevalent in Swiss pet cats. We sought to
investigate the presence and clinical importance of “Candidatus Mycoplasma turicensis” infection
in pet cats outside of Switzerland and to perform the molecular characterization of isolates from
different countries. A “Candidatus Mycoplasma turicensis”-specific real-time PCR assay was
applied to blood samples from 426 United Kingdom (UK), 147 Australian, and 69 South African
pet cats. The 16S rRNA genes of isolates from different countries were sequenced and
signalment and laboratory data for the cats were evaluated for associations with
“Candidatus Mycoplasma turicensis” infection. Infections were detected in samples from UK,
Australian, and South African pet cats. Infection was associated with the male gender, and
“Candidatus Mycoplasma haemominutum” and M. haemofelis coinfection. Coinfected cats
exhibited significantly lower packed cell volume (PCV) values than uninfected cats. Phylogenetic
analyses revealed that some Australian and South African “CandidatusMycoplasma turicensis”
isolates branched away from the remaining isolates. In summary, “Candidatus Mycoplasma
turicensis” infection in pet cats exists over a wide geographical area and significantly decreased
PCV values are observed in cats coinfected with other feline hemoplasmas.

12.)Molecular Characterization of Novel G5 Bovine Rotavirus Strains

By: Sunghee- Park/ DOI: 10.1128/JCM.01196-06 (2006)

Group A rotaviruses are a major cause of acute gastroenteritis in young children as well as many
domestic animals. The rotavirus genome is composed of 11 segments of double-stranded RNA
and can undergo genetic reassortment during mixed infections, leading to progeny viruses with
novel or atypical phenotypes. The aim of this study was to determine if the bovine group A
rotavirus strains KJ44 and KJ75, isolated from clinically infected calves, share genetic features
with viruses obtained from heterologous species. All 11 genes sequences of the KJ44 and KJ75
strains were sequenced and analyzed. The KJ44 VP4 had 91.7% to 96.3% deduced amino acid
identity to the bovine related P[1] strain, whereas the KJ75 strain was most closely related to the
bovine related P[5] strain (91.9% to 96.9% amino acid identity). Both KJ44 and KJ75 strains also
contained the bovine related VP3 gene. The remaining 9 segments were closely related to porcine
group A rotaviruses. The KJ44 and KJ75 strains showed high amino acid identity to the G5
rotaviruses, sharing 90.4% to 99.0% identity. In addition, these strains belonged to the NSP4
genotype B, which is typical of porcine rotaviruses and subgroup I, with the closest relationship
to the porcine JL-94 strain. These results strongly suggest that bovine rotavirus strains with the
G5 genotype occur in nature as a novel G genotype in cattle as a result of a natural reassortment
between bovine and porcine strains.

13.)Presence of Pathogenicity Island Genes in Enterococcus faecalis Isolates from Pigs in Denmark

By: Nathan Shankar/ DOI: 10.1128/JCM.01218-06 (2006)

Enterococcus faecalis isolates of porcine origin were screened for the presence of a previously
identified pathogenicity island (PAI). By using the esp gene as a genetic marker for the presence
of this PAI, 9 esp-positive and 10 esp-negative isolates of porcine origin were investigated by use
of a designed oligonucleotide array. The results indicated the clustering of esp-positive strains by
multilocus sequence typing (MLST), but surprisingly, all strains investigated contained parts of
the PAI. None of the strains of animal origin investigated belonged to previously identified MLST
complex 2, where most isolates from patients cluster. Five of the nine esp-positive E.
faecalis isolates of animal origin belonged to the same PAI complex as human isolate MMH594
but differed in their sequence types, which strongly indicates the horizontal transfer of the PAI
between enterococci of porcine and human origin.
 14.)Comparison of Subtyping Methods for Differentiating Salmonella entericaSerovar Typhimurium
Isolates Obtained from Food Animal Sources.

By: Steven L. Foley/ DOI: 10.1128/JCM.00745-06 (2006)

Molecular characterization (e.g., DNA-based typing methods) of Salmonella isolates is frequently

employed to compare and distinguish clinical isolates recovered from animals and from patients
with food-borne disease and nosocomial infections. In this study, we compared the abilities of
different phenotyping and genotyping methods to distinguish isolates of Salmonella
enterica serovar Typhimurium from different food animal sources. One hundred twenty-eight S.
enterica serovar Typhimurium strains isolated from cattle, pigs, chickens, and turkeys or derived
food products were characterized using pulsed-field gel electrophoresis (PFGE), repetitive
element PCR (Rep-PCR), multilocus sequence typing (MLST), plasmid profiling, and antimicrobial
susceptibility testing. Among the 128 Salmonella isolates tested, we observed 84 Rep-PCR
profiles, 86 PFGE patterns, 89 MLST patterns, 36 plasmid profiles, and 38 susceptibility profiles.
The molecular typing methods, i.e., PFGE, MLST, and Rep-PCR, demonstrated the best
discriminatory power among Salmonella isolates. However, no apparent correlation was evident
between the results of one molecular typing method and those of the others, suggesting that a
combination of multiple methods is needed to differentiate S. entericaserovar Typhimurium
isolates that genetically cluster according to one particular typing method.

15.)Isolation of Corynebacterium xerosis from Animal Clinical Specimens

By: Vale E. Gracia/ DOI: 10.1128/JCM.02473-05 (2006)

This article describes the first identification of Corynebacterium xerosis from animal clinical
specimens, which was confirmed by microbiological and molecular genetic (16S rRNA gene
sequencing) methods.
Corynebacterium xerosis is considered a commensal microorganism of human skin and mucous
membranes. There are a limited number of reports associating C. xerosis with different human
infections (1, 6), but it has been demonstrated that most of the C. xerosis isolates identified in the
routine clinical laboratory represent Corynebacterium amycolatum strains (5, 6). Therefore, true
human clinical isolates of C. xerosis are extremely rare (8), and there are no reports of its isolation
from animals. We report the isolation and biochemical and genetic identification of eight strains
of C. xerosis from different animal clinical specimens.
The eight isolates identified in this study were recovered from different clinical specimens routinely
submitted for microbiological diagnosis to the Exopol laboratory in Zaragoza, Spain. Clinical
specimens were collected under aseptic conditions and cultured aerobically on Columbia sheep
blood agar (Oxoid España, Madrid, Spain) for 24 to 48 h at 37°C. For all clinical specimens, C.
xerosis was recovered in moderate to high numbers in pure culture or as the predominant isolate
from normally sterile body locations. Details of the clinical isolates are given in Table 1. Although
only eight isolates were biochemically and genetically identified, coryneform bacteria similar to
isolates St33874, St34960, St38671, and St49327 (similar colony morphology on sheep blood
agar plates and similar Gram stain morphology) were also recovered from other organs from the
same animal or different animals in the same disease episode. Thus, coryneform bacteria similar
to isolate St33874 were also recovered in pure culture from the liver, spleen, and kidney of the
same animal and from the liver of a second pig. A coryneform bacterium similar to isolate St34960
was also recovered in pure culture from the liver of the same animal. A coryneform bacterium
similar to St38671 was also isolated from the joint of another pig; in this case, Mycoplasma
hyosinoviae was also detected by immunocytochemistry. Coryneform bacteria similar to isolate
St49327 were also recovered in pure culture from the liver and kidney of the same animal.

CONCLUSION
Research and thesis papers about Microbiology from 2006 focused more on Veterinarian
Microbiology like isolation of animal clinical specimens and new discovered antibiotic resistance,
identification of gene regulations and clearer understanding in Neurological Diseases.

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