bluuebunny/crossref_metadata_2025 huggingface dataset:
Climate dynamics of a hard snowball Earth
Authors: Pierrehumbert R. T.
Published: January 2005

The problem of deglaciating a globally ice‐covered (“hard snowball”) Earth is examined using a series of general circulation model simulations. The aim is to determine the amount of CO2 that must be accumulated in the atmosphere in order to trigger deglaciation. Prior treatments of this problem have been limited to energy balance models, which are incapable of treating certain crucial physical processes that turn out to strongly affect the conditions under which deglaciation can occur. CO2 concentrations up to .2 bars are considered in the general circulation model simulations, and even at such high CO2 content the model radiation code is found to perform well in comparison with codes explicitly designed for high CO2. In contrast to prevailing expectations, the hard snowball Earth is found to be nearly 30 K short of deglaciation, even at .2 bars. The very cold climates arise from a combination of the extreme seasonal and diurnal cycle, lapse rate effects, snow cover, and weak cloud effects. Several aspects of the atmospheric dynamics are examined in detail. The simulations indicate that the standard scenario, wherein snowball termination occurs after a few tenths of a bar of CO2 has built up following cessation of weathering, is problematic. However, the climate was found to be sensitive to details of a number of parameterized physical processes, notably clouds and heat transfer through the stable boundary layer. It is not out of the question that other parameterization suites might permit deglaciation. The results should not be construed as meaning that the hard snowball state could not have occurred, but only that deglaciation requires the operation of as‐yet undiscovered processes that would enhance the climate sensitivity. A brief survey of some of the possibilities is provided.
Comparison of ground‐based and Total Ozone Mapping Spectrometer erythemal UV doses at the island of Lampedusa in the period 1998–2003: Role of tropospheric aerosols
Authors: Meloni D. , di Sarra A. , Herman J. R. , Monteleone F. , Piacentino S.
Published: January 2005

The Total Ozone Mapping Spectrometer (TOMS) has the longest time series of globally distributed estimates of UV irradiance at the Earth's surface. The proper interpretation of TOMS estimated irradiances relies on well‐calibrated and well‐maintained spectrometers at the Earth's surface. In this study, daily erythemal irradiances measured by a Brewer spectrophotometer at the island of Lampedusa (35.5°N, 12.6°E), in the Mediterranean are compared with TOMS observations in the period January 1998 to August 2003. The comparison, also because of the peculiar conditions at Lampedusa, a very good site for ground‐based validation of satellite observations, allows us to recognize how the space‐borne observations are influenced by the presence of atmospheric aerosols. Two TOMS data sets, derived applying different algorithms to retrieve ozone and UV irradiance from the backscattered radiance, are used in this study: Version 7 (V7) and the recently developed version 8 (V8), which uses new climatologies for ozone and temperature profiles and accounts for the attenuation by tropospheric aerosols through the aerosol index (AI). As shown in previous studies performed with V7 TOMS data, satellite‐derived erythemal doses systematically overestimate ground‐based measurements, mainly because of uncorrected absorption by aerosols in the troposphere. The bias between the TOMS and Brewer doses for all‐sky conditions is (9.4 ± 19.8)% for V7 and (7.3 ± 20.0)% for V8 and decreases to (5.6 ± 8.0)% for V7 and (3.4 ± 8.4)% for V8 for the cloud‐free cases. The large standard deviations for all‐sky conditions are due to nonhomogeneity in the cloud cover within the sensor field of view, while those for cloud‐free days are caused by the large aerosol variability occurring at Lampedusa. The biases for cloud‐free days have been related to differences in the TOMS AI UV attenuation algorithm and to the aerosol optical depth (AOD) at 415.6 nm measured with a Sun photometer at Lampedusa since 2001. The mean bias between the V7 TOMS and Brewer doses progressively increases with AI and AOD at 415.6 nm, from ± 3% for low AI and AOD up to 21% for 1.5 ≤ AI < 2.5 and 0.5 ≤ AOD < 0.6. The bias calculated with V8 data set varies between +6% for 0 ≤ AI < 1 and about −8% for 4 ≤ AI < 5, well within the respective uncertainties of the Brewer and TOMS measurements. TOMS V8 data show a smaller dependency on the aerosol absorption, indicating that the implemented corrections produce more reliable estimated doses. For very low aerosol loading (AOD at 415.6 nm below 0.2), the TOMS‐to‐Brewer erythemal dose ratio, both for V7 and V8, is approximately 1, indicating that the radiometric calibration of the Brewer instrument is consistent with the TOMS estimated irradiances from derived ozone and Rayleigh scattering attenuation.
Second quantization method in the presence of bound states of particles
Authors: Peletminskii Sergey V. , Slyusarenko Yuriy V.
Published: January 2005

We develop an approximate second quantization method for describing the many-particle systems in the presence of bound states of particles at low energies (the kinetic energy of particles is small in comparison to the binding energy of compound particles). In this approximation the compound and elementary particles are considered on an equal basis. This means that creation and annihilation operators of compound particles can be introduced. The Hamiltonians, which specify the interactions between compound and elementary particles and between compound particles themselves, are found in terms of the interaction amplitudes for elementary particles. The nonrelativistic quantum electrodynamics is developed for systems containing both elementary and compound particles. Some applications of this theory are considered.
New CO–CO interaction potential tested by rovibrational calculations
Authors: Vissers G. W. M. , Heßelmann A. , Jansen G. , Wormer P. E. S. , van der Avoird A.
Published: January 2005

A four-dimensional potential energy surface (PES) for the CO dimer consisting of rigid molecules has been calculated, using a scheme that combines density functional theory to describe the monomers and symmetry adapted perturbation theory for the interaction energy (DFT-SAPT). The potential is fitted in terms of analytic functions, and the fitted potential is used to compute the lowest rovibrational states of the dimer. The quality of the PES is comparable to that of a previously published surface [G. W. M. Vissers, P. E. S. Wormer, and A. van der Avoird, Phys. Chem. Chem. Phys., 5, 4767 (2003)], which was calculated with the coupled cluster single double and perturbative triples [CCSD(T)] method. It is shown that a weighted average of the DFT-SAPT and the CCSD(T) potential gives results that are in very good agreement with experimental data, for both (12CO)2 and (13CO)2. The relative weight was determined by adjusting the energy gap between the origins of the lowest two stacks of rotational levels of (12CO)2 to the measured value.
Exact solutions of the isoholonomic problem and the optimal control problem in holonomic quantum computation
Authors: Tanimura Shogo , Nakahara Mikio , Hayashi Daisuke
Published: January 2005

The isoholonomic problem in a homogeneous bundle is formulated and solved exactly. The problem takes a form of a boundary value problem of a variational equation. The solution is applied to the optimal control problem in holonomic quantum computer. We provide a prescription to construct an optimal controller for an arbitrary unitary gate and apply it to a k-dimensional unitary gate which operates on an N-dimensional Hilbert space with N⩾2k. Our construction is applied to several important unitary gates such as the Hadamard gate, the CNOT gate, and the two-qubit discrete Fourier transformation gate. Controllers for these gates are explicitly constructed.
Human Fanconi anemia monoubiquitination pathway promotes homologous DNA repair
Authors: Nakanishi Koji , Yang Yun-Gui , Pierce Andrew J. , Taniguchi Toshiyasu , Digweed Martin , D'Andrea Alan D. , Wang Zhao-Qi , Jasin Maria
Published: January 2005

Fanconi anemia (FA) is a recessive disorder characterized by congenital abnormalities, progressive bone-marrow failure, and cancer susceptibility. Cells from FA patients are hypersensitive to agents that produce DNA crosslinks and, after treatment with these agents, have pronounced chromosome breakage and other cytogenetic abnormalities. Eight
FANC
genes have been cloned, and the encoded proteins interact in a common cellular pathway. DNA-damaging agents activate the monoubiquitination of FANCD2, resulting in its targeting to nuclear foci that also contain BRCA1 and BRCA2/FANCD1, proteins involved in homology-directed DNA repair. Given the interaction of the FANC proteins with BRCA1 and BRCA2, we tested whether cells from FA patients (groups A, G, and D2) and mouse
Fanca
–/–
cells with a targeted mutation are impaired for this repair pathway. We find that both the upstream (FANCA and FANCG) and downstream (FANCD2) FA pathway components promote homology-directed repair of chromosomal double-strand breaks (DSBs). The FANCD2 monoubiquitination site is critical for normal levels of repair, whereas the ATM phosphorylation site is not. The defect in these cells, however, is mild, differentiating them from BRCA1 and BRCA2 mutant cells. Surprisingly, we provide evidence that these proteins, like BRCA1 but unlike BRCA2, promote a second DSB repair pathway involving homology, i.e., single-strand annealing. These results suggest an early role for the FANC proteins in homologous DSB repair pathway choice.
AML1-ETO
and
C-KIT
mutation/overexpression in t(8;21) leukemia: Implication in stepwise leukemogenesis and response to Gleevec
Authors: Wang Yue-Ying , Zhou Guang-Biao , Yin Tong , Chen Bing , Shi Jing-Yi , Liang Wen-Xue , Jin Xiao-Long , You Jian-Hua , Yang Guang , Shen Zhi-Xiang , Chen Jue , Xiong Shu-Min , Chen Guo-Qiang , Xu Feng , Liu Yi-Wei , Chen Zhu , Chen Sai-Juan
Published: January 2005

To explore the genetic abnormalities that cooperate with
AML1-ETO
(
AE
) fusion gene to cause acute myeloid leukemia (AML) with t(8;21), we screened a number of candidate genes and identified 11 types of mutations in
C-KIT
gene (
mC-KIT
), including 6 previously undescribed ones among 26 of 54 (48.1%) cases with t(8;21). To address a possible chronological order between
AE
and
mC-KIT,
we showed that, among patients with
AE
and
mC-KIT
, most leukemic cells at disease presentation harbored both genetic alteration, whereas in three such cases investigated during complete remission, only
AE
, but not
mC-KIT
, could be detected by allele-specific PCR. Therefore,
mC-KIT
should be a subsequent event on the basis of t(8;21). Furthermore, induced expression of
AE
in U937-A/E cells significantly up-regulated mRNA and protein levels of C-KIT. This may lead to an alternative way of
C-KIT
activation and may explain the significantly higher
C-KIT
expression in 81.3% of patients with t(8;21) than in patients with other leukemias. These data strongly suggest that t(8;21) AML follows a stepwise model in leukemogenesis, i.e.,
AE
represents the first, fundamental genetic hit to initiate the disease, whereas activation of the C-KIT pathway may be a second but also crucial hit for the development of a full-blown leukemia. Additionally, Gleevec suppressed the C-KIT activity and induced proliferation inhibition and apoptosis in cells bearing
C-KIT
N822K mutation or overexpression, but not in cells with D816
mC-KIT
. Gleevec also exerted a synergic effect in apoptosis induction with cytarabine, thus providing a potential therapeutic for t(8;21) leukemia.
Effect of some factors on the fusion rate of bovine–rabbit interspecies reconstructed eggs
Authors: Xiao-Rong Zhang , Ya Liu , Yun-Hai Zhang , Da-Yuan Chen , Li Lian , Jin-Song Li , Ren-Tao Jin , Zhi-Guo Zhang , Mei-Ling Zhang , Cun-Li Wang
Published: January 2005

Tests were conducted to highlight the effects of donor cell treatment (bovine G0- and non-G0 phase somatic cells refrigerated for 1–5 or 12–14 days at 4°C), fusion solution (with or without cytochalasin B) and age of the rabbit (young, 3–5-months old; or multiparous, 10–12 months old) as oocyte donor on the fusion and mortality rates of bovine–rabbit interspecies reconstructed eggs. Results showed that there were no significant differences (P>0.05) in fusion and mortality rates of eggs reconstructed with G0 cells or non-G0 cells as nuclear donor somatic cells. The same was also true when nuclear donor somatic cells (G0 cells or non-G0 cells) were treated at low temperature (4°C) for 1–5 or 12–14 days. The fusion rate of reconstructed eggs did not change significantly (P>0.05) when adding cytochalasin B into the fusion solution, but the mortality rate increased significantly (P<0.05). No significant effect (P>0.05) was found in fusion rate of the eggs reconstructed with young rabbits' and multiparous rabbits' oocytes as recipient, but the mortality rate decreased significantly (P<0.01) for young rabbit oocytes compared with multiparous rabbit ones.
Identification of oxalate oxidase in rice defence system against rice blast
Authors: Jie Feng , Makoto Takano
Published: January 2005

A rice cDNA library was screened using OSK3 protein kinase as bait in a yeast two-hybrid system. The gene encoding oxalate oxidase was one of the positive clones interacting with OSK3 protein kinase. The interactions were verified by detecting expression of the reporter gene lacZ. The results suggest that oxalate oxidase is a downstream element in the disease resistance signal cascade mediated by OSK3 protein kinase in rice.
Variation analysis of the ORF5 gene of Porcine reproductive and respiratory syndrome virus
Authors: Zhi-Qiang Gao , Xin Guo , Zhen-Lin Cha , Yan-Hong Chen , Han-Chun Yang
Published: January 2005

Three Porcine reproductive and respiratory syndrome virus (PRRSV) isolates (HB-1(sh)/2002, HB-2(sh)/2002 and JX-1/2002) were obtained from pig farms in Hebei and Jiangxi provinces, China. The complete ORF5 gene of the isolates was amplified using RT-PCR and sequenced. It was shown that ORF5 genes of all isolates encoded 200 amino acids. Comparing ORF5 genes of the three isolates and published sequences for five other PRRSV isolates in China, variation analysis showed that all of the isolates were of the American genotype, with 88.2–99.0% amino acid identity. ORF5 genes among BJ-4, S1 and J1 had higher similarity, sharing 98–99% identity of the deduced amino acids. HB-1(sh)/2002, HB-2(sh)/2002 and JX-1/2002 and CH-1a presented 92–96% identity among their ORF5 genes. Phylogenetic analysis revealed that these isolates could be divided into two subgroups based on the genetic distance of their ORF5 gene: the first subgroup comprised BJ-4, S1 and J1 and was closer to VR2332 and vaccine strains; the second included HB-1(sh)/2002, HB-2(sh)/2002, JX-1/2002 and CH-1a.
Determinant formulas for class numbers in function fields
Authors: Jung Hwanyup , Bae Sunghan , Ahn Jaehyun
Published: January 2005

In this paper, by extending Kucera’s idea to the function field case, we obtain several determinant formulas involving the real class number and the relative class number of any subfield of cyclotomic function fields. We also provide several examples using these determinant formulas.
A primitive trinomial of degree 6972593
Authors: Brent Richard , Larvala Samuli , Zimmermann Paul
Published: January 2005

The only primitive trinomials of degree

6972593
6972593

over

GF
⁡
(
2
)

\operatorname {GF}(2)

are

x

6972593

+

x

3037958

+
1

x^{6972593} + x^{3037958} + 1

and its reciprocal.
Linear difference equations with transition points
Authors: Wang Z. , Wong R.
Published: January 2005

Two linearly independent asymptotic solutions are constructed for the second-order linear difference equation
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="y Subscript n plus 1 Baseline left-parenthesis x right-parenthesis minus left-parenthesis upper A Subscript n Baseline x plus upper B Subscript n Baseline right-parenthesis y Subscript n Baseline left-parenthesis x right-parenthesis plus y Subscript n minus 1 Baseline left-parenthesis x right-parenthesis equals 0 comma">

y

n
+
1

(
x
)
−
(

A
n

x
+

B
n

)

y
n

(
x
)
+

y

n
−
1

(
x
)
=
0
,

\begin{equation} y_{n+1}(x)-(A_nx+B_n)y_n(x)+y_{n-1}(x)=0, \nonumber \end{equation}

where

A
n

A_n

and

B
n

B_n

have power series expansions of the form
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="upper A Subscript n Baseline tilde sigma-summation Underscript s equals 0 Overscript normal infinity Endscripts StartFraction alpha Subscript s Baseline Over n Superscript s Baseline EndFraction comma upper B Subscript n Baseline tilde sigma-summation Underscript s equals 0 Overscript normal infinity Endscripts StartFraction beta Subscript s Baseline Over n Superscript s Baseline EndFraction">

A
n

∼

∑

s
=
0

∞

α
s

n
s

,

B
n

∼

∑

s
=
0

∞

β
s

n
s

\begin{equation} A_n\sim \sum ^\infty _{s=0}\frac {\alpha _s}{n^s}, \qquad \qquad B_n\sim \sum ^\infty _{s=0}\frac {\beta _s}{n^s}\nonumber \end{equation}

with

α
0

≠
0

\alpha _0\ne 0

. Our results hold uniformly for

x
x

in an infinite interval containing the transition point

x
+

x_+

given by

α
0

x
+

+

β
0

=
2

\alpha _0 x_++\beta _0=2

. As an illustration, we present an asymptotic expansion for the monic polynomials

π
n

(
x
)

\pi _n(x)

which are orthogonal with respect to the modified Jacobi weight

w
(
x
)
=
(
1
−
x

)
α

(
1
+
x

)
β

h
(
x
)

w(x)=(1-x)^\alpha (1+x)^\beta h(x)

,

x
∈
(
−
1
,
1
)

x\in (-1,1)

, where

α
\alpha

,

β
>
−
1

\beta >-1

and

h
h

is real analytic and strictly positive on

[
−
1
,
1
]

[-1, 1]

.
A fast sweeping method for Eikonal equations
Authors: Zhao Hongkai
Published: January 2005

In this paper a fast sweeping method for computing the numerical solution of Eikonal equations on a rectangular grid is presented. The method is an iterative method which uses upwind difference for discretization and uses Gauss-Seidel iterations with alternating sweeping ordering to solve the discretized system. The crucial idea is that each sweeping ordering follows a family of characteristics of the corresponding Eikonal equation in a certain direction simultaneously. The method has an optimal complexity of

O
(
N
)

O(N)

for

N
N

grid points and is extremely simple to implement in any number of dimensions. Monotonicity and stability properties of the fast sweeping algorithm are proven. Convergence and error estimates of the algorithm for computing the distance function is studied in detail. It is shown that

2

n

2^{n}

Gauss-Seidel iterations is enough for the distance function in

n
n

dimensions. An estimation of the number of iterations for general Eikonal equations is also studied. Numerical examples are used to verify the analysis.
More on the total number of prime factors of an odd perfect number
Authors: Hare Kevin
Published: January 2005

Let

σ
(
n
)

\sigma (n)

denote the sum of the positive divisors of

n
n

. We say that

n
n

is perfect if

σ
(
n
)
=
2
n

\sigma (n) = 2 n

. Currently there are no known odd perfect numbers. It is known that if an odd perfect number exists, then it must be of the form

N
=

p
α

∏

j
=
1

k

q
j

2

β
j

N = p^\alpha \prod _{j=1}^k q_j^{2 \beta _j}

, where

p
,

q
1

,
…
,

q
k

p, q_1, \ldots , q_k

are distinct primes and

p
≡
α
≡
1

(
mod

4
)

p \equiv \alpha \equiv 1 \pmod {4}

. Define the total number of prime factors of

N
N

as

Ω
(
N
)
:=
α
+
2

∑

j
=
1

k

β
j

\Omega (N) := \alpha + 2 \sum _{j=1}^k \beta _j

. Sayers showed that

Ω
(
N
)
≥
29

\Omega (N) \geq 29

. This was later extended by Iannucci and Sorli to show that

Ω
(
N
)
≥
37

\Omega (N) \geq 37

. This paper extends these results to show that

Ω
(
N
)
≥
47

\Omega (N) \geq 47

.
On variational approximations in quantum molecular dynamics
Authors: Lubich Christian
Published: January 2005

The Dirac-Frenkel-McLachlan variational principle is the basic tool for obtaining computationally accessible approximations in quantum molecular dynamics. It determines equations of motion for an approximate time-dependent wave function on an approximation manifold of reduced dimension. This paper gives a near-optimality result for variational approximations. It bounds the error in terms of the distance of the exact wave function to the approximation manifold and identifies the parameters that control the deviation of the variational approximation from the best approximation on the manifold.
On standardized models of isogenous elliptic curves
Authors: Siksek Samir
Published: January 2005

Let

E
,
 

E
′

E,~E^\prime

be isogenous elliptic curves over

Q

{\mathbb Q}

given by standardized Weierstrass models. We show that (in the obvious notation)
\[

a
1
′

=

a
1

,

a
2
′

=

a
2

,

a
3
′

=

a
3

a_1’ =a_1, \qquad a_2’ = a_2, \qquad a_3’ = a_3

\]
and, moreover, that there are integers

t
,
 
w

t,~w

such that
\[

a
4
′

=

a
4

−
5
t
 
and
 

a
6
′

=

a
6

−

b
2

t
−
7
w
,

a_4’ = a_4 - 5t~\text {and}~ a_6’ = a_6 - b_2 t - 7w,

\]
where

b
2

=

a
1
2

+
4

a
2

b_2=a_1^2+4 a_2

.
Computing multiple roots of inexact polynomials
Authors: Zeng Zhonggang
Published: January 2005

We present a combination of two algorithms that accurately calculate multiple roots of general polynomials. Algorithm I transforms the singular root-finding into a regular nonlinear least squares problem on a pejorative manifold, and it calculates multiple roots simultaneously from a given multiplicity structure and initial root approximations. To fulfill the input requirement of Algorithm I, we develop a numerical GCD-finder containing a successive singular value updating and an iterative GCD refinement as the main engine of Algorithm II that calculates the multiplicity structure and the initial root approximation. While limitations exist in certain situations, the combined method calculates multiple roots with high accuracy and consistency in practice without using multiprecision arithmetic, even if the coefficients are inexact. This is perhaps the first blackbox-type root-finder with such capabilities. To measure the sensitivity of the multiple roots, a structure-preserving condition number is proposed and error bounds are established. According to our computational experiments and error analysis, a polynomial being ill-conditioned in the conventional sense can be well conditioned with the multiplicity structure being preserved, and its multiple roots can be computed with high accuracy.
On solving composite power polynomial equations
Authors: Wu Yingquan , Hadjicostis Christoforos
Published: January 2005

It is well known that a system of power polynomial equations can be reduced to a single-variable polynomial equation by exploiting the so-called Newton’s identities. In this work, by further exploring Newton’s identities, we discover a binomial decomposition rule for composite elementary symmetric polynomials. Utilizing this decomposition rule, we solve three types of systems of composite power polynomial equations by converting each type to single-variable polynomial equations that can be solved easily. For each type of system, we discuss potential applications and characterize the number of nontrivial solutions (up to permutations) and the complexity of our proposed algorithmic solution.
A new family of stable mixed finite elements for the 3D Stokes equations
Authors: Zhang Shangyou
Published: January 2005

A natural mixed-element approach for the Stokes equations in the velocity-pressure formulation would approximate the velocity by continuous piecewise-polynomials and would approximate the pressure by discontinuous piecewise-polynomials of one degree lower. However, many such elements are unstable in 2D and 3D. This paper is devoted to proving that the mixed finite elements of this

P

k

\mathbf {P}_k

-

P

k
−
1

P_{k-1}

type when

k
≥
3

k \ge 3

satisfy the stability condition—the Babuška-Brezzi inequality on macro-tetrahedra meshes where each big tetrahedron is subdivided into four subtetrahedra. This type of mesh simplifies the implementation since it has no restrictions on the initial mesh. The new element also suits the multigrid method.
Computing isogeny covariant differential modular forms
Authors: Hurlburt Chris
Published: January 2005

We present the computation modulo

p
2

p^2

and explicit formulas for the unique isogeny covariant differential modular form of order one and weight

χ

−
p
−
1
,
−
p

\chi _{-p-1,-p}

called

f

j
e
t

f_{\mathrm {jet}}

, an isogeny covariant differential modular form of order two and weight

χ

−

p
2

−
p
,
−
1
,
−
1

\chi _{-p^2-p,-1,-1}

denoted by

f

j
e
t

h

j
e
t

f_{\mathrm {jet}}h_{\mathrm {jet}}

, and an isogeny covariant differential modular form

h

j
e
t

h_{\mathrm {jet}}

of order two and weight

χ

1
−

p
2

,
0
,
−
1

\chi _{1-p^2,0,-1}

.
Numerical indefinite integration by double exponential sinc method
Authors: Tanaka Ken’ichiro , Sugihara Masaaki , Murota Kazuo
Published: January 2005

We present a numerical method for approximating an indefinite integral by the double exponential sinc method. The approximation error of the proposed method with

N
N

integrand function evaluations is
\[

O

(
exp
⁡
(
−

c
1

N

/

log
⁡
(

c
2

N
)
)
)

\mathrm {O}(\exp (-c_1 N/\log (c_2 N)))

\]
for a reasonably wide class of integrands, including those with endpoint singularities. The proposed method compares favorably with the existing formulas based on the ordinary sinc method. Computational results show the accordance of the actual convergence rates with the theoretical estimate.
Brevundimonas mediterranea sp. nov., a non-stalked species from the Mediterranean Sea
Authors: Fritz Ingo , Strömpl Carsten , Nikitin Denis I. , Lysenko A. M. , Abraham Wolf-Rainer
Published: January 2005

Six strains of Gram-negative, rod-shaped, non-spore-forming bacteria were isolated from the Mediterranean Sea. 16S rRNA gene sequence analysis indicated that the strains were affiliated within the alphaproteobacterial genusBrevundimonas, withBrevundimonas intermedia(99·4 %) andBrevundimonas vesicularis(99·2 %) as their closest relatives. This affiliation was supported by chemotaxonomic data (major polar lipids: phosphatidyl diacylglycerol, sulfoquinovosyl diacylglycerol and phosphatidyl glucopyranosyl diacylglycerol; major fatty acids: C18 : 1, C16 : 0, C16 : 1, C15 : 0, C17 : 1ω8c, 11-Me-C18 : 1ω5t). The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of the strains from all recognizedBrevundimonasspecies. The strains therefore represent a novel species, for which the nameBrevundimonas mediterraneasp. nov. is proposed, with the type strain V4.BO.10T(=LMG 21911T=CIP 107934T).
‘Candidatus Mycoplasma haematoparvum’, a novel small haemotropic mycoplasma from a dog
Authors: Sykes Jane E. , Ball Louise M. , Bailiff Nathan L. , Fry Michael M.
Published: January 2005

A novel small haemoplasma was detected following cytological examination of blood smears from a splenectomized dog with haemic neoplasia. The 16S rRNA and rnpB genes of the organism were partially sequenced and a phylogenetic tree constructed. The organism was most closely related to the small feline haemoplasma, ‘Candidatus Mycoplasma haemominutum’ (94 % 16S rRNA gene nucleotide sequence identity; 75 % rnpB) and was only distantly related to Mycoplasma haemocanis (78 % 16S rRNA gene nucleotide sequence identity; 65 % rnpB). As this organism has not been cultured in vitro, the candidate species name ‘Candidatus Mycoplasma haematoparvum’ is proposed.
Phylogenetic analysis of the genera Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium on the basis of 16S rRNA gene and internally transcribed spacer region sequences
Authors: Kwon Soon-Wo , Park Jin-Young , Kim Jong-Shik , Kang Jun-Won , Cho Yang-Hee , Lim Chun-Keun , Parker Matthew A. , Lee Gil-Bok
Published: January 2005

A total of 128 strains was isolated from more than 23 legume hosts in Korea. Phylogenetic relationships between these Korean isolates and reference strains of the genera Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium were analysed using their 16S rRNA gene and internally transcribed spacer (ITS) region sequences. Among the Bradyrhizobium strains, dendrograms based on both the 16S rRNA gene and ITS region sequences produced two main groups. The ITS tree yielded at least two new clusters that were discernable from the seven previously delineated genospecies. Large discrepancies were revealed between phylogenetic dendrograms based on 16S rRNA gene and ITS region sequences for members of the genus Rhizobium, reflecting their taxonomic heterogeneity. The amalgamation of Rhizobium and former members of Agrobacterium was confirmed using the 16S rRNA tree. Phylogenetic analysis of ITS region sequences showed that the Rhizobium giardinii clade (group II) and the Rhizobium radiobacter/Rhizobium rubi clade (group III) could be tentatively recognized as groups that are separable from the core group (group I), which includes Rhizobium leguminosarum. Dendrograms based on the 16S rRNA gene and ITS region sequences of Mesorhizobium strains were highly conflicting due to the poor taxonomic resolution of the 16S rRNA gene sequences and the low confidence in the ITS dendrogram. Several Korean isolates within the genus Mesorhizobium are thought to represent novel taxa when considering their relatively low ITS region sequence similarities (<80 %) to the reference strains.
Arthrobacter bergerei sp. nov. and Arthrobacter arilaitensis sp. nov., novel coryneform species isolated from the surfaces of cheeses
Authors: Irlinger Françoise , Bimet François , Delettre Jérome , Lefèvre Martine , Grimont Patrick A. D.
Published: January 2005

Fourteen isolates of two different bacterial species isolated from the surface of smear-ripened cheeses were found to exhibit many characteristics of the genus Arthrobacter. The isolates were aerobic, Gram-positive, catalase-positive, non-spore-forming and non-motile. The cell-wall peptidoglycan contained lysine, alanine and glutamic acid. rrs sequence analysis indicated that the new isolates Re117T and Ca106T are closely related to the Arthrobacter nicotianae group and showed highest sequence similarity (>98 %) to Arthrobacter nicotianae and Arthrobacter protophormiae. However, DNA–DNA hybridization studies indicated that the strains represented two novel genomic species within the genus Arthrobacter and did not belong to A. nicotianae or A. protophormiae (<43 % DNA–DNA relatedness). On the basis of the phylogenetic and phenotypic distinctiveness of the new isolates, these bacteria should be classified as two novel Arthrobacter species, for which the names Arthrobacter bergerei sp. nov. and Arthrobacter arilaitensis sp. nov. are proposed. Type strains have been deposited in culture collections as Arthrobacter bergerei Ca106T (=CIP 108036T=DSM 16367T) and Arthrobacter arilaitensis Re117T (=CIP 108037T=DSM 16368T).
Application of sliding-window discretization and minimization of stochastic complexity for the analysis of fAFLP genotyping fingerprint patterns of Vibrionaceae
Authors: Dawyndt Peter , Thompson Fabiano L. , Austin Brian , Swings Jean , Koski Timo , Gyllenberg Mats
Published: January 2005

Minimization of stochastic complexity (SC) was used as a method for classification of genotypic fingerprints. The method was applied to fluorescent amplified fragment length polymorphism (fAFLP) fingerprint patterns of 507Vibrionaceaerepresentatives. As the current BinClass implementation of the optimization algorithm for classification only works on binary vectors, the original fingerprints were discretized in a preliminary step using the sliding-window band-matching method, in order to maximally preserve the information content of the original band patterns. The novel classification generated using the BinClass software package was subjected to an in-depth comparison with a hierarchical classification of the same dataset, in order to acknowledge the applicability of the new classification method as a more objective algorithm for the classification of genotyping fingerprint patterns. Recent DNA–DNA hybridization and 16S rRNA gene sequence experiments proved that the classification based on SC-minimization forms separate clusters that contain the fAFLP patterns for all representatives of the speciesEnterovibrio norvegicus,Vibrio fortis,Vibrio diazotrophicusorVibrio campbellii, while previous hierarchical cluster analysis had suggested more heterogeneity within the fAFLP patterns by splitting the representatives of the above-mentioned species into multiple distant clusters. As a result, the new classification methodology has highlighted some previously unseen relationships within the biodiversity of the familyVibrionaceae.
Paenibacillus xylanilyticus sp. nov., an airborne xylanolytic bacterium
Authors: Rivas Raúl , Mateos Pedro F. , Martínez-Molina Eustoquio , Velázquez Encarna
Published: January 2005

During a search for xylan-degrading micro-organisms, a sporulating bacterium was recovered from xylan-containing agar plates exposed to air in a research laboratory (Salamanca University, Spain). The airborne isolate (designated strain XIL14T) was identified by 16S rRNA gene sequencing as representing a Paenibacillus species most closely related to Paenibacillus illinoisensis JCM 9907T (99·3 % sequence similarity) and Paenibacillus pabuli DSM 3036T (98 % sequence similarity). Phenotypic, chemotaxonomic and DNA–DNA hybridization data indicated that the isolate belongs to a novel species of the genus Paenibacillus. Cells of strain XIL14T were motile, sporulating, rod-shaped, Gram-positive and facultatively anaerobic. The predominant cellular fatty acids were anteiso-C15 : 0 and C16 : 0. The DNA G+C content of strain XIL14T was 50·5 mol%. Growth was observed with many carbohydrates, including xylan, as the only carbon source and gas production was not observed from glucose. Catalase was positive and oxidase was negative. The airborne isolate produced a variety of hydrolytic enzymes, including xylanases, amylases, gelatinase and β-galactosidase. DNA–DNA hybridization levels between strain XIL14T and P. illinoisensis DSM 11733T and P. pabuli DSM 3036T were 43·3 and 36·3 %, respectively. According to the data obtained, strain XIL14T is considered to represent a novel species for which the name Paenibacillus xylanilyticus sp. nov. is proposed (=LMG 21957T=CECT 5839T).
Proposal of the genus Thermoactinomyces sensu stricto and three new genera, Laceyella, Thermoflavimicrobium and Seinonella, on the basis of phenotypic, phylogenetic and chemotaxonomic analyses
Authors: Yoon Jung-Hoon , Kim In-Gi , Shin Yong-Kook , Park Yong-Ha
Published: January 2005

Phylogenetic analysis based on 16S rRNA gene sequences revealed that Thermoactinomyces species with validly published names can be assigned to four clusters or lineages. The type strains of Thermoactinomyces sacchari and Thermoactinomyces putidus were differentiated from the type strains of Thermoactinomyces vulgaris and Thermoactinomyces intermedius by the predominant menaquinone and fatty acid profiles. The type strains of Thermoactinomyces dichotomicus and Thermoactinomyces peptonophilus formed lines of descent distinct from other Thermoactinomyces species. Thermoactinomyces dichotomicus KCTC 3667T was distinguishable from the type strains of Thermoactinomyces vulgaris and Thermoactinomyces intermedius by the contents of two fatty acids, iso-C16 : 0 and iso-C17 : 0. Thermoactinomyces dichotomicus could be distinguished from other Thermoactinomyces species by DNA G+C content and some phenotypic properties, particularly its property of forming a yellow colour. The type strain of Thermoactinomyces peptonophilus was distinguishable from other Thermoactinomyces species by differences in menaquinone profile, major fatty acids, DNA G+C content and some physiological properties including optimal growth temperature. On the basis of these data, the creation of three new genera, Laceyella, Thermoflavimicrobium and Seinonella, is proposed in addition to the genus Thermoactinomyces sensu stricto. The genus Laceyella gen. nov. is proposed to accommodate Thermoactinomyces sacchari and Thermoactinomyces putidus as Laceyella sacchari comb. nov. and Laceyella putida comb. nov., the genus Thermoflavimicrobium gen. nov. is proposed for Thermoactinomyces dichotomicus as Thermoflavimicrobium dichotomicum comb. nov. and the genus Seinonella gen. nov. is proposed for Thermoactinomyces peptonophilus as Seinonella peptonophila comb. nov.
A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model
Authors: Devulder G. , de Montclos M. Pérouse , Flandrois J. P.
Published: January 2005

Advances in DNA sequencing and the increasing number of sequences available in databases have greatly enhanced the bacterial identification process. Several species within the genusMycobacteriumcause serious human and animal diseases. In order to assess their relative positions in the evolutionary process, four gene fragments, from the 16S rRNA (564 bp),hsp65(420 bp),rpoB(396 bp) andsod(408 bp) genes, were sequenced from 97 strains, including all available type strains of the genusMycobacterium. The results demonstrate that, in this case, the concatenation of different genes allows significant increases in the power of discrimination and the robustness of the phylogenetic tree. The sequential and/or combined use of sequences of several genes makes it possible to refine the phylogenetic approach and provides a molecular basis for accurate species identification.
Erythrobacter seohaensis sp. nov. and Erythrobacter gaetbuli sp. nov., isolated from a tidal flat of the Yellow Sea in Korea
Authors: Yoon Jung-Hoon , Oh Tae-Kwang , Park Yong-Ha
Published: January 2005

Two Gram-negative, non-spore-forming, slightly halophilic strains, SW-135Tand SW-161T, which were isolated from a tidal flat of the Yellow Sea in Korea, were subjected to a polyphasic taxonomic study. The two isolates lacked bacteriochlorophyllaand contained ubiquinone-10 (Q-10) as the predominant respiratory lipoquinone and C18 : 1ω7cand C17 : 1ω6cas the major fatty acids. The DNA G+C contents of strains SW-135Tand SW-161Twere 62·2 and 64·5 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that the two strains fall within the radiation of the cluster comprisingErythrobacterspecies. Strains SW-135Tand SW-161Texhibited a 16S rRNA gene sequence similarity value of 96·9 % and a mean DNA–DNA relatedness level of 12·3 %. Sequence similarities between strains SW-135Tand SW-161Tand the type strains of recognizedErythrobacterspecies ranged from 96·7 to 98·5 %. Levels of DNA–DNA relatedness were low enough to indicate that strains SW-135Tand SW-161Trepresent members of two species separate from all recognizedErythrobacterspecies. On the basis of polyphasic taxonomic data, strains SW-135T(=KCTC 12228T=DSM 16221T) and SW-161T(=KCTC 12227T=DSM 16225T) were classified as two novelErythrobacterspecies, for which the namesErythrobacter seohaensissp. nov. andErythrobacter gaetbulisp. nov. are proposed, respectively.
Marinobacter bryozoorum sp. nov. and Marinobacter sediminum sp. nov., novel bacteria from the marine environment
Authors: Romanenko Lyudmila A. , Schumann Peter , Rohde Manfred , Zhukova Natalia V. , Mikhailov Valery V. , Stackebrandt Erko
Published: January 2005

Two marine, Gram-negative, aerobic, halophilic strains, designated KMM 3657T and KMM 3840T, were isolated and found to be phylogenetically closely related to each other, showing 96·6 % 16S rRNA gene sequence similarity. Both strains are members of the genus Marinobacter in the γ-Proteobacteria (94·7–98·0 % 16S rRNA gene sequence similarity). Strain KMM 3657T and Marinobacter lipolyticus SM19T were closely related, with 98·0 % sequence similarity. The novel strains shared generic physiological and chemotaxonomic properties with Marinobacter species, but differed in their temperature range for growth, inability to grow in 20 % NaCl and at >43 °C, metabolic properties and fatty acid composition. On the basis of phenotypic and phylogenetic analysis data, it is proposed that the strains represent two novel species, Marinobacter bryozoorum sp. nov., with the type strain KMM 3840T (=50-11T=DSM 15401T), and Marinobacter sediminum sp. nov., with the type strain KMM 3657T (=R65T=DSM 15400T).
Isolation of Lentibacillus salicampi strains and Lentibacillus juripiscarius sp. nov. from fish sauce in Thailand
Authors: Namwong Sirilak , Tanasupawat Somboon , Smitinont Thitapha , Visessanguan Wonnop , Kudo Takuji , Itoh Takashi
Published: January 2005

Eight strains of aerobic, spore-forming, Gram-positive, moderately halophilic bacteria were isolated from sauce (nam-pla and bu-du) produced in Thailand by the fermentation of fish. They grew optimally in the presence of 10 % NaCl, at 37 °C and pH 7·0. A diagnostic diamino acid, meso-diaminopimelic acid, was present in the cell-wall peptidoglycan. The predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C15 : 0 and iso-C16 : 0. Phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid were found to be the major polar lipid components. The DNA G+C content was 42–43 mol%. These bacteria were further divided into two groups based on phenotypic characteristics and DNA–DNA similarities. Three strains of Group I were highly affiliated to the type strain of Lentibacillus salicampi in terms of phenotypic characterization and DNA–DNA similarities (96–102 %); accordingly, they were identified as strains of L. salicampi. A representative strain of Group II, strain IS40-3T, was most closely related to L. salicampi in terms of 16S rRNA-based phylogenetic analysis, although five strains of Group II could be distinguished from L. salicampi by means of several phenotypic properties, low 16S rRNA gene sequence similarity (95·2 %) and low DNA–DNA similarities (12–32 %). Therefore, the Group II strains should be included in a novel species of the genus Lentibacillus, for which the name Lentibacillus juripiscarius sp. nov. is proposed. The type strain is IS40-3T (=JCM 12147T=PCU 229T=TISTR 1535T).
Salinimonas chungwhensis gen. nov., sp. nov., a moderately halophilic bacterium from a solar saltern in Korea
Authors: Jeon Che Ok , Lim Jee-Min , Park Dong-Jin , Kim Chang-Jin
Published: January 2005

A halophilic non-spore-forming bacterium of the γ-Proteobacteria, designated strain BH030046T, was isolated from a solar saltern in Korea. Cells were Gram-negative, chemoheterotrophic, short rod-shaped and motile with a polar flagellum. Comparative 16S rRNA gene sequence analysis revealed that strain BH030046T formed a distinct lineage in the family Alteromonadaceae and was distinguished from its closest related genera Alteromonas (91·4–94·8 %), Aestuariibacter (92·1–93·5 %) and Glaciecola (92·1–93·5 %) on the basis of low 16S rRNA gene sequence similarities. Physiological and biochemical data also showed that the isolate was different from members of these three genera. The predominant cellular fatty acids were C16 : 0 and C18 : 1
ω7c. DNA G+C content was 48 mol% and the major isoprenoid quinone was Q-8. The strain grew optimally at 30–35 °C, pH 7·0–8·0 and 2–5 % NaCl. On the basis of physiological and molecular properties, strain BH030046T (=KCTC 12239T=DSM 16280T) represents a novel genus and species in the family Alteromonadaceae, for which the name Salinimonas chungwhensis gen. nov., sp. nov. is proposed.
Desulfovibrio putealis sp. nov., a novel sulfate-reducing bacterium isolated from a deep subsurface aquifer
Authors: Basso Odile , Caumette Pierre , Magot Michel
Published: January 2005

A novel sulfate-reducing bacterium was isolated from a well that collected water from a deep aquifer at a depth of 430 m in the Paris Basin, France. The strain, designated B7-43T, was made up of vibrioid cells that were motile by means of a single polar flagellum. Cells contained desulfoviridin. In the presence of sulfate, the following substrates were used as energy and carbon sources: lactate, pyruvate, malate, fumarate, ethanol, butanol, acetate/H2 and glycine. Sulfite and thiosulfate were also used as electron acceptors in the presence of lactate. In the absence of electron acceptors, pyruvate, malate and fumarate were fermented. Optimal growth was obtained in 1 g NaCl l−1 and at pH 7. On the basis of 16S rRNA gene sequence analysis, the isolate was most closely related to members of the genus Desulfovibrio (90 % similarity). It is thus proposed that strain B7-43T (=DSM 16056T=ATCC BAA-905T) represents a novel species within this genus, Desulfovibrio putealis sp. nov.
Winogradskyella thalassocola gen. nov., sp. nov., Winogradskyella epiphytica sp. nov. and Winogradskyella eximia sp. nov., marine bacteria of the family Flavobacteriaceae
Authors: Nedashkovskaya Olga I. , Kim Seung Bum , Han Suk Kyun , Snauwaert Cindy , Vancanneyt Marc , Swings Jean , Kim Kyung-Ok , Lysenko Anatoly M. , Rohde Manfred , Frolova Galina M. , Mikhailov Valery V. , Bae Kyung Sook
Published: January 2005

Three novel heterotrophic, Gram-negative, yellow-pigmented, aerobic, gliding, oxidase- and catalase-positive bacteria were isolated from algae collected in the Gulf of Peter the Great, Sea of Japan. 16S rRNA gene sequence analysis revealed that the strains studied represented members of the familyFlavobacteriaceaeand showed 93·5–93·8 % similarity with their closest relative,Psychroserpens burtonensis. The DNA G+C content of the strains was 34–37 mol%. The major respiratory quinone was MK-6. The predominant fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1, iso-C16 : 0-3OH and iso-C17 : 0-3OH. On the basis of their phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, the newly described bacteria have been assigned to the new genusWinogradskyellagen. nov., asWinogradskyella thalassocolasp. nov. (type strain, KMM 3907T=KCTC 12221T=LMG 22492T=DSM 15363T),Winogradskyella epiphyticasp. nov. (type strain, KMM 3906T=KCTC 12220T=LMG 22491T=CCUG 47091T) andWinogradskyella eximiasp. nov. (type strain, KMM 3944T(=KCTC 12219T=LMG 22474T).
Bacillus velezensis sp. nov., a surfactant-producing bacterium isolated from the river Vélez in Málaga, southern Spain
Authors: Ruiz-García Cristina , Béjar Victoria , Martínez-Checa Fernando , Llamas Inmaculada , Quesada Emilia
Published: January 2005

Two Gram-positive, endospore-forming bacterial strains, CR-502T and CR-14b, which produce surfactant molecules are described. Phenotypic tests and phylogenetic analyses showed these strains to be members of the genus Bacillus and related to the species Bacillus atrophaeus, Bacillus mojavensis, Bacillus subtilis, Bacillus vallismortis and Bacillus amyloliquefaciens, although they differ from these species in a number of phenotypic characteristics. DNA–DNA hybridization confirmed that they show less than 20 % hybridization with the above-mentioned species and therefore represent a novel species of Bacillus. The DNA G+C content is 46·4 mol% in strain CR-502T and 46·1 mol% in strain CR-14b. The main fatty acids in strain CR-502T are 15 : 0 anteiso (32·70 %), 15 : 0 iso (29·86 %) and 16 : 0 (13·41 %). The main quinone in strain CR-502T is MK-7 (96·6 %). In the light of the polyphasic evidence gathered in this study, it is proposed that these strains be classified as a novel species of the genus Bacillus, with the name Bacillus velezensis sp. nov. The type strain (CR-502T=CECT 5686T=LMG 22478T) was isolated from a brackish water sample taken from the river Vélez at Torredelmar in Málaga, southern Spain.