bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient Sulfide Assimilation in Methanosarcina acetivorans Is Mediated by the MA1715 Protein
Authors: Rauch Benjamin Julius , Perona John J. 
Published: May 2016

ABSTRACT

Conserved genes essential to sulfur assimilation and trafficking in aerobic organisms are missing in many methanogens, most of which inhabit highly sulfidic, anaerobic environmental niches. This suggests that methanogens possess distinct pathways for the synthesis of key metabolites and intermediates, including cysteine, homocysteine, and protein persulfide groups. Prior work identified a novel tRNA-dependent two-step pathway for cysteine biosynthesis and a new metabolic transformation by which sulfur is inserted into aspartate semialdehyde to produce homocysteine. Homocysteine biosynthesis requires two of the three proteins previously identified in our laboratory by a comprehensive bioinformatics approach. Here, we show that the third protein identified
in silico
, the ApbE-like protein COG2122, facilitates sulfide assimilation in
Methanosarcina acetivorans
. Knockout strains lacking the gene encoding COG2122 are severely impaired for growth when sulfide is provided as the sole sulfur source. However, rapid growth is recovered upon supplementation with cysteine, homocysteine, or cystathionine, suggesting that COG2122 is required for efficient biosynthesis of both cysteine and homocysteine. Deletion of the gene encoding COG2122 does not influence the extent of sulfur modifications in tRNA or the prevalence of iron-sulfur clusters, indicating that the function of COG2122 could be limited to sulfide assimilation for cysteine and homocysteine biosynthesis alone.

IMPORTANCE
We have found that the conserved
M. acetivorans
ma1715
gene, which encodes an ApbE-like protein, is required for optimal growth with sulfide as the sole sulfur source and supports both cysteine and homocysteine biosynthesis
in vivo
. Together with related functional-genomics studies in methanogens, these findings make a key contribution to elucidating the novel pathways of sulfide assimilation and sulfur trafficking in anaerobic microorganisms that existed before the advent of oxygenic photosynthesis. The data suggest that the MA1715 protein is particularly important to sustaining robust physiological function when ambient sulfide concentrations are low. Phylogenetic analysis shows that MA1715 and other recently discovered methanogen sulfur-trafficking proteins share an evolutionary history with enzymes in the methanogenesis pathway. The newly characterized genes thus likely formed an essential part of the core metabolic machinery of the ancestral euryarchaeote.
Coexpression of Escherichia coli obgE, Encoding the Evolutionarily Conserved Obg GTPase, with Ribosomal Proteins L21 and L27
Authors: Maouche Rim , Burgos Hector L. , My Laetitia , Viala Julie P. , Gourse Richard L. , Bouveret Emmanuelle 
Published: May 2016

ABSTRACT

Multiple essential small GTPases are involved in the assembly of the ribosome or in the control of its activity. Among them, ObgE (CgtA) has been shown recently to act as a ribosome antiassociation factor that binds to ppGpp, a regulator whose best-known target is RNA polymerase. The present study was aimed at elucidating the expression of
obgE
in
Escherichia coli
. We show that
obgE
is cotranscribed with ribosomal protein genes
rplU
and
rpmA
and with a gene of unknown function,
yhbE
. We show here that about 75% of the transcripts terminate before
obgE
, because there is a transcriptional terminator between
rpmA
and
yhbE
. As expected for ribosomal protein operons, expression was highest during exponential growth, decreased during entry into stationary phase, and became almost undetectable thereafter. Expression of the operon was derepressed in mutants lacking ppGpp or DksA. However, regulation by these factors appears to occur post-transcription initiation, since no effects of ppGpp and DksA on
rplU
promoter activity were observed
in vitro
.

IMPORTANCE
The conserved and essential ObgE GTPase binds to the ribosome and affects its assembly. ObgE has also been reported to impact chromosome segregation, cell division, resistance to DNA damage, and, perhaps most interestingly, persister formation and antibiotic tolerance. However, it is unclear whether these effects are related to its role in ribosome formation. Despite its importance, no studies on ObgE expression have been reported. We demonstrate here that
obgE
is expressed from an operon encoding two ribosomal proteins, that the operon's expression varies with the growth phase, and that it is dependent on the transcription regulators ppGpp and DksA. Our results thus demonstrate that
obgE
expression is coupled to ribosomal gene expression.
Loss of PodJ in Agrobacterium tumefaciens Leads to Ectopic Polar Growth, Branching, and Reduced Cell Division
Authors: Anderson-Furgeson James C. , Zupan John R. , Grangeon Romain , Zambryski Patricia C. 
Published: May 2016

ABSTRACT

Agrobacterium tumefaciens
is a rod-shaped Gram-negative bacterium that elongates by unipolar addition of new cell envelope material. Approaching cell division, the growth pole transitions to a nongrowing old pole, and the division site creates new growth poles in sibling cells. The
A. tumefaciens
homolog of the
Caulobacter crescentus
polar organizing protein PopZ localizes specifically to growth poles. In contrast, the
A. tumefaciens
homolog of the
C. crescentus
polar organelle development protein PodJ localizes to the old pole early in the cell cycle and accumulates at the growth pole as the cell cycle proceeds. FtsA and FtsZ also localize to the growth pole for most of the cell cycle prior to Z-ring formation. To further characterize the function of polar localizing proteins, we created a deletion of
A. tumefaciens
podJ
(

podJ
At

). Δ

podJ
At

cells display ectopic growth poles (branching), growth poles that fail to transition to an old pole, and elongated cells that fail to divide. In Δ

podJ
At

cells,
A. tumefaciens
PopZ-green fluorescent protein (PopZ
At
-GFP) persists at nontransitioning growth poles postdivision and also localizes to ectopic growth poles, as expected for a growth-pole-specific factor. Even though GFP-PodJ
At
does not localize to the midcell in the wild type, deletion of

podJ
At

impacts localization, stability, and function of Z-rings as assayed by localization of FtsA-GFP and FtsZ-GFP. Z-ring defects are further evidenced by minicell production. Together, these data indicate that PodJ
At
is a critical factor for polar growth and that Δ

podJ
At

cells display a cell division phenotype, likely because the growth pole cannot transition to an old pole.

IMPORTANCE
How rod-shaped prokaryotes develop and maintain shape is complicated by the fact that at least two distinct species-specific growth modes exist: uniform sidewall insertion of cell envelope material, characterized in model organisms such as
Escherichia coli
, and unipolar growth, which occurs in several alphaproteobacteria, including
Agrobacterium tumefaciens
. Essential components for unipolar growth are largely uncharacterized, and the mechanism constraining growth to one pole of a wild-type cell is unknown. Here, we report that the deletion of a polar development gene,

podJ
At

, results in cells exhibiting ectopic polar growth, including multiple growth poles and aberrant localization of cell division and polar growth-associated proteins. These data suggest that PodJ
At
is a critical factor in normal polar growth and impacts cell division in
A. tumefaciens
.
Alternative Translation Initiation of a Haloarchaeal Serine Protease Transcript Containing Two In-Frame Start Codons
Authors: Tang Wei , Wu Yufeng , Li Moran , Wang Jian , Mei Sha , Tang Bing , Tang Xiao-Feng 
Published: May 2016

ABSTRACT

Recent studies have shown that haloarchaea employ leaderless and Shine-Dalgarno (SD)-less mechanisms for translation initiation of leaderless transcripts with a 5′ untranslated region (5′ UTR) of <10 nucleotides (nt) and leadered transcripts with a 5′ UTR of ≥10 nt, respectively. However, whether the two mechanisms can operate on the same naturally occurring haloarchaeal transcript carrying multiple potential start codons is unknown. In this study, the transcript of the
sptA
gene (encoding an extracellular serine protease of
Natrinema
sp. strain J7-2) was experimentally determined and found to contain two potential in-frame AUG codons (AUG
1
and AUG
2
) located 5 and 29 nt, respectively, downstream of the transcription start site. Mutational analysis revealed that both AUGs can function as the translation start codon for production of active SptA, although AUG
1
is more efficient than AUG
2
for translation initiation. Insertion of a stable stem-loop structure between the two AUGs completely abolished initiation at AUG
1
but did not affect initiation at AUG
2
, indicating that AUG
2
-initiated translation does not involve ribosome scanning from the 5′ end of the transcript. Furthermore, the efficiency of AUG
2
-initiated translation was not influenced by an upstream SD-like sequence. In addition, both AUG
1
and AUG
2
contribute to transcript stability, probably by recruiting ribosomes to protect the transcript against degradation. These data suggest that depending on which of two in-frame start codons is used, the
sptA
transcript can act as either a leaderless or a leadered transcript for SptA production in haloarchaea.

IMPORTANCE
In eukaryotes and bacteria, alternative translation start sites contribute to proteome complexity and can be used as a functional mechanism to increase translation efficiency. However, little is known about alternative translation initiation in archaea. Our results demonstrate that leaderless and SD-less mechanisms can be used for translation initiation of the
sptA
transcript from two in-frame start codons, raising the possibility that in haloarchaea, alternative translation initiation on one transcript functions to increase translation efficiency and/or contribute to proteome complexity.
Growth Inhibition by External Potassium of Escherichia coli Lacking PtsN (EIIA
Ntr
) Is Caused by Potassium Limitation Mediated by YcgO
Authors: Sharma Ravish , Shimada Tomohiro , Mishra Vinod K. , Upreti Suchitra , Sardesai Abhijit A. 
Published: May 2016

ABSTRACT

The absence of PtsN, the terminal phosphoacceptor of the phosphotransferase system comprising PtsP-PtsO-PtsN, in
Escherichia coli
confers a potassium-sensitive (K
s
) phenotype as the external K
+
concentration ([K
+
]
e
) is increased above 5 mM. A growth-inhibitory increase in intracellular K
+
content, resulting from hyperactivated Trk-mediated K
+
uptake, is thought to cause this K
s
. We provide evidence that the K
s
of the Δ
ptsN
mutant is associated with K
+
limitation. Accordingly, the moderate K
s
displayed by the Δ
ptsN
mutant was exacerbated in the absence of the Trk and Kup K
+
uptake transporters and was associated with reduced cellular K
+
content. Conversely, overproduction of multiple K
+
uptake proteins suppressed the K
s
. Expression of PtsN variants bearing the H73A, H73D, and H73E substitutions of the phosphorylation site histidine of PtsN complemented the K
s
. Absence of the predicted inner membrane protein YcgO (also called CvrA) suppressed the K
s
, which was correlated with elevated cellular K
+
content in the Δ
ptsN
mutant, but the Δ
ptsN
mutation did not alter YcgO levels. Heterologous overexpression of
ycgO
also led to K
s
that was associated with reduced cellular K
+
content, exacerbated by the absence of Trk and Kup and alleviated by overproduction of Kup. Our findings are compatible with a model that postulates that K
s
in the Δ
ptsN
mutant occurs due to K
+
limitation resulting from activation of K
+
efflux mediated by YcgO, which may be additionally stimulated by [K
+
]
e
, implicating a role for PtsN (possibly its dephosphorylated form) as an inhibitor of YcgO activity.

IMPORTANCE
This study examines the physiological link between the phosphotransferase system comprising PtsP-PtsO-PtsN and K
+
ion metabolism in
E. coli
. Studies on the physiological defect that renders an
E. coli
mutant lacking PtsN to be growth inhibited by external K
+
indicate that growth impairment results from cellular K
+
limitation that is mediated by YcgO, a predicted inner membrane protein. Additional observations suggest that dephospho-PtsN may inhibit and external K
+
may stimulate K
+
limitation mediated by YcgO. It is speculated that YcgO-mediated K
+
limitation may be an output of a response to certain stresses, which by modulating the phosphotransfer capacity of the PtsP-PtsO-PtsN phosphorelay leads to growth cessation and stress tolerance.
More Flexible Curve Matching via the Partial Fréchet Similarity
Authors: Scheffer Christian 
Published: May 2016

We study a modified version of the partial Fréchet similarity that is motivated by real world applications, e.g. the analysis of spectroscopic data in the context of astroinformatics and the analysis of birds’ migration trajectories. In those practical applications of curve matching it is often necessary to ignore outliers while dissimilarities regarding individual directions should be weighted by individual costs. We enable both by computing the partial Fréchet similarity between polygonal curves w.r.t. a non-uniform metric. In particular, we measure distances by a function [Formula: see text] that is induced by a set of weighted vectors. We discuss the approximation quality of [Formula: see text] regarding any [Formula: see text] metric and present a polynomial time algorithm for computing an exact solution of the resulting modified partial Fréchet similarity.
Stable recovery of sparse signals with coherent tight frames via lp-analysis approach
Authors: Liu Dekai , Li Song 
Published: May 2016

In this paper, we consider to recover a signal which is sparse in terms of a tight frame from undersampled measurements via [Formula: see text]-minimization problem for [Formula: see text]. In [Compressed sensing with coherent tight frames via [Formula: see text]-minimization for [Formula: see text], Inverse Probl. Imaging 8 (2014) 761–777], Li and Lin proved that when [Formula: see text] there exists a [Formula: see text], depending on [Formula: see text] such that for any [Formula: see text], each solution of the [Formula: see text]-minimization problem can approximate the true signal well. The constant [Formula: see text] is referred to as the [Formula: see text]-RIP constant of order [Formula: see text] which was first introduced by Candès et al. in [Compressed sensing with coherent and redundant dictionaries, Appl. Comput. Harmon. Anal. 31 (2011) 59–73]. The main aim of this paper is to give the closed-form expression of [Formula: see text]. We show that for every [Formula: see text]-RIP constant [Formula: see text], if [Formula: see text] where [Formula: see text] then the [Formula: see text]-minimization problem can reconstruct the true signal approximately well. Our main results also hold for the complex case, i.e. the measurement matrix, the tight frame and the signal are all in the complex domain. It should be noted that the[Formula: see text]-RIP condition is independent of the coherence of the tight frame (see [Compressed sensing with coherent and redundant dictionaries, Appl. Comput. Harmon. Anal. 31 (2011) 59–73]). In particular, when the tight frame reduces to an identity matrix or an orthonormal matrix, the conclusions in our paper coincide with the results appeared in [Stable recovery of sparse signals via [Formula: see text]-minimization, Appl. Comput. Harmon. Anal. 38 (2015) 161–176].
Dupuytren's Contracture. The Safety and Efficacy of Collagenase Treatment
Authors: Odinsson Adalsteinn , Brenne Lars Erik , Lurie Tone Bøyesen , Finsen Vilhjalmur 
Published: May 2016

Background: Our main goal was to see if treatment with collagenase injection is safe and effective and to assess patient satisfaction with this new treatment. Methods: We prospectively followed 77 consecutive patients, treated for contracture in 91 fingers and 142 joints that received total of 109 collagenase injections. The patients were reviewed on the first and second day and at 4 and 12 months. A contracture reduced to five degrees or less at 12 months after the last injection, was considered to be a successful outcome. Results: A mean of 1.2 injections were used per patient and 0.8 injections per joint. There was a significant improvement in mean passive extension deficit. Out of the 142 joints treated, 84 (59%) met our criterion for a successful outcome; 56 (80%) out of 70 MCP joints and 28 (39%) out of 72 PIP joints. There were also significant improvements in both hand function and pain. No serious adverse events were observed. The mean patient satisfaction with the treatment at the 12-month follow up was a VAS score of 78 (0 = none; 100 = complete) and only 11% stated that they would not have consented to the treatment if they had known the outcome in advance. Conclusions: Treatment of Dupuytren's disease with collagenase injection is both safe and effective. It is now our primary treatment for Dupuytren's disease.
Recovery of Wrist Function after Volar Locking Plate Fixation for Distal Radius Fractures
Authors: Takeuchi Naohide , Hotokezaka Shunsuke , Okada Takamitsu , Yuge Hidehiko , Mae Takao , Iwamoto Yukihide 
Published: May 2016

Background: The purpose of our present study was to examine the recovery of the postoperative wrist function, and to compare the range of motion among each direction ofthe wrist joint during the same time periods after surgery for distal radius fractures.Methods: Twenty patients treated with a volar locking plate were evaluated. The active range of motion and grip strength were assessed at four weeks, six weeks, three months, six months and one year after surgery.Results: The ratio of the range of motion in pronation and supination recovered significantly earlier than for any other directions within six months after surgery (p = 0.0205), however, the ratio of the range of motion among the six directions was not significantly different at one year after surgery (p = 0.0823). The recovery of the range of motion in flexion was 96.8% compared with the contralateral wrist at one year after surgery, and it was not significantly lower than that in extension, radial deviation or ulnar deviation (97.8%, 93.5%, 94.4%, respectively). The grip strength of dominant hand recovered from 50% after four weeks to 66% after six weeks, 83% after three months, 91% after six months and 106% at the examination performed after one year compared with the uninjured non-dominant hand. The grip strength of non-dominant hand recovered from 52% after four weeks to 59% after six weeks, 79% after three months, 84% after six months and 94% at the examination performed after one year compared with the uninjured dominant hand. The mean DASH score was 5.3.Conclusions: The range of motion in flexion can achieve similar improvement to that in the other directions by obtaining the appropriate postoperative parameters. The optimal postoperative radiographic parameters were thus identified to be essential for successfully obtaining a recovery of the wrist function for unstable distal radius fractures.
Computer Aided Assessment in Microsurgical Training
Authors: Lahiri Amitabha , Sebastin Sandeep Jacob , Yusoff Siti Khadijah , Sze Chong Alphonsus Khin 
Published: May 2016

Background: Acquiring competence in microsurgical suturing is a basic requirement for any trainee aspiring to perform clinical microsurgery. New methods and simulation platform continue to evolve, but the assessment of the quality of microsurgical suturing is largely subjective. We present the concept of computer aided assessment of standardised microsurgical task, using a novel training platform. The platform comprises of a simulator (hardware) that provides the trainee standardised microsurgical tasks, which are then evaluated using a customised software. Methods: A cohort of trainees attending a five day microsurgery training course was selected. The trainees performed three standardised exercises on the platform, on the first third and the fifth day of the course. All the exercises were subjected to computer aided assessment. Results: Trainees demonstrated a learning curve over the five day period through the evaluation system, with initial increase in performance followed by a plateau. Eighty four percent of the trainees were able to achieve acceptable scores. Sixteen percent of the trainees were unable to perform a suturing of acceptable quality at the end of the training (fifth day). Conclusions: The mean scores correlated with the level of difficulty of the exercise. We conclude that computer aided assessment can provide an objective view of the quality of suturing as well as skill maintenance in for trainees.
An Anechoic Space at the Carpal Tunnel Inlet is a Consistent Ultrasonographic Entity which Accommodates Tendon Displacement during Finger Flexion
Authors: Lee Bing Howe , Goh Chin Hock , Lahiri Amitabha 
Published: May 2016

Background: We consistently observed the presence of anechoic spaces on standard ultrasonographic imaging of the carpal tunnel inlet in normal subjects. These spaces change in size during finger flexion and have not been characterized in a large sample of normal individuals. Ultrasonographic quantification of these spaces may indicate the available space in the region of the carpal tunnel, which allows the normal motion of tendons and the median nerve. Methods: Transverse ultrasonographic images of the carpal tunnel inlet from 33 asymptomatic volunteers were obtained at Position A (fingers in extension) and B (fingers in flexion). Cross-sectional area (CSA), perimeter and position of anechoic space relative to median nerve were recorded. Results: Analysis showed a 75.4% prevalence rate of a single anechoic space. Two discrete patterns were observed. 89.1% had a decrease in CSA and perimeter of anechoic space from Position A to B while 10.9% exhibited an increase. Mean position of the anechoic space is ulnar (7.49 ± 3.57 mm) and dorsal (2.18 ± 1.28 mm) to the median nerve. Conclusions: A consistent anechoic space at the carpal tunnel inlet is seen in 75.4% of normal hands and can be quantified (cross sectional area 11.75 ± 7.36 mm2). It allows for the accommodation of flexor tendons during finger flexion.
The “Trigger” Thumb Locked in Extension – An Unusual Presentation of a Common Paediatric Condition
Authors: Johnstone Bruce R. , Currie L. J. , Ek Edmund W. , Wilks Daniel J. , McCombe David B. , Coombs Christopher J. 
Published: May 2016

Background: We report a variant of paediatric trigger thumb which is locked in extension rather than flexion. Methods: Eleven children with 14 trigger thumbs (three bilateral) locked in extension were reviewed retrospectively over a 12-year period. The number of flexed trigger thumbs encountered over this period was established from the operating room database. Results: All children were treated with release of the A1 pulley. Nine children achieved a full range of motion at the interphalangeal joint. One child with bilateral extended trigger thumbs required bilateral dorsal capsulotomy and another child developed temporary mild triggering in flexion. Conclusions: Approximately 1% of trigger thumbs treated operatively at this institution presented as the extended variant. Trigger thumb locked in extension should be considered in a child presenting with inability to flex the thumb.