bluuebunny/crossref_metadata_2025_split huggingface dataset:
The nature of the CO2‐concentrating mechanisms in a marine diatom, Thalassiosira pseudonana
Authors: Clement Romain , Dimnet Laura , Maberly Stephen C. , Gontero Brigitte 
Published: November 2015

Summary

Diatoms are widespread in aquatic ecosystems where they may be limited by the supply of inorganic carbon. Their carbon dioxide‐concentrating mechanisms (CCMs) involving transporters and carbonic anhydrases (CAs) are well known, but the contribution of a biochemical CCM involving C4 metabolism is contentious.

The CCM(s) present in the marine‐centric diatom, Thalassiosira pseudonana, were studied in cells exposed to high or low concentrations of CO2, using a range of approaches.

At low CO2, cells possessed a CCM based on active uptake of CO2 (70% contribution) and bicarbonate, while at high CO2, cells were restricted to CO2. CA was highly and rapidly activated on transfer to low CO2 and played a key role because inhibition of external CA produced uptake kinetics similar to cells grown at high CO2. The activities of phosphoenolpyruvate (PEP) carboxylase (PEPC) and the PEP‐regenerating enzyme, pyruvate phosphate dikinase (PPDK), were lower in cells grown at low than at high CO2. The ratios of PEPC and PPDK to ribulose bisphosphate carboxylase were substantially lower than 1, even at low CO2.

Our data suggest that the kinetic properties of this species results from a biophysical CCM and not from C4 type metabolism.
Functional ratios among leaf, xylem and phloem areas in branches change with shade tolerance, but not with local light conditions, across temperate tree species
Authors: Zhang Lan , Copini Paul , Weemstra Monique , Sterck Frank 
Published: November 2015

Summary

Leaf, xylem and phloem areas drive the water and carbon fluxes within branches and trees, but their mutual coordination is poorly understood. We test the hypothesis that xylem and phloem areas increase relative to leaf area when species are selected for, or branches are exposed to, higher levels of light intensity.

Trees of 10 temperate, broadleaved and deciduous, tree species were selected. Fifty‐centimetre‐long branches were collected from shaded and exposed conditions at a height of 3–4 m. We measured the total leaf area, xylem area, phloem area and leaf traits, as well as the area of the constituent cell types, for a stem section at the branch base.

Xylem area : leaf area and phloem area : leaf area ratios did not differ consistently between sun and shade branches, but, as expected, they decreased with species' shade tolerance. Similar trends were observed for conductive cell areas in xylem and phloem.

Trees of light‐demanding species maintain higher water loss and carbon gain rates per leaf area by producing more xylem area and phloem area than shade‐tolerant species. We call for more comparative branch studies as they provide an integrated biological perspective on functional traits and their role in the ecology of tree species.
Recent assembly of the global herbaceous flora: evidence from the paper daisies (Asteraceae: Gnaphalieae)
Authors: Nie Ze‐Long , Funk Vicki A. , Meng Ying , Deng Tao , Sun Hang , Wen Jun 
Published: November 2015

Summary

The global flora is thought to contain a large proportion of herbs, and understanding the general spatiotemporal processes that shaped the global distribution of these communities is one of the most difficult issues in biogeography.

We explored patterns of world‐wide biogeography in a species‐rich herbaceous group, the paper daisy tribe Gnaphalieae (Asteraceae), based on the hitherto largest taxon sampling, a total of 835 terminal accessions representing 80% of the genera, and encompassing the global geographic range of the tribe, with nuclear internal transcribed spacer (ITS) and external transcribed spacer (ETS) sequences.

Biogeographic analyses indicate that Gnaphalieae originated in southern Africa during the Oligocene, followed by repeated migrations into the rest of Africa and the Mediterranean region, with subsequent entries into other continents during various periods starting in the Miocene.

Expansions in the late Miocene to Pliocene appear to have been the driving force that shaped the global distribution of the tribe as forests were progressively broken up by the mid‐continent aridification and savannas and grasslands expanded into the interior of the major continents. This pattern of recent colonizations may explain the world‐wide distribution of many other organisms in open ecosystems and it is highlighted here as an emerging pattern in the evolution of the global flora.
Farewell to Political Obligation: In Defense of a Permissive Conception of Legitimacy
Authors: Zhu Jiafeng 
Published: November 2015

AbstractIn the recent debate on political legitimacy, we have seen the emergence of a revisionist camp, advocating the idea of ‘legitimacy without political obligation,’ as opposed to the traditional view that political obligation is necessary for state legitimacy. The revisionist idea of legitimacy is appealing because if it stands, the widespread skepticism about the existence of political obligation will not lead us to conclude that the state is illegitimate. Unfortunately, existing conceptions of ‘legitimacy without political obligation’ are subject to serious objections. In this article, I propose a new conception of ‘legitimacy without political obligation,’ and defend it against various objections that the revisionist idea of legitimacy is either conceptually or morally mistaken. This new conception of legitimacy promises to advance the debates between anarchists and statists by making the task of philosophical anarchists significantly more difficult.
Rab9A is required for delivery of cargo from recycling endosomes to melanosomes
Authors: Mahanty Sarmistha , Ravichandran Keerthana , Chitirala Praneeth , Prabha Jyothi , Jani Riddhi Atul , Setty Subba Rao gangi 
Published: November 2015

SummaryMelanosomes are a type of lysosome‐related organelle that is commonly defective in Hermansky–Pudlak syndrome. Biogenesis of melanosomes is regulated by BLOC‐1, ‐2, ‐3, or AP‐1, ‐3 complexes, which mediate cargo transport from recycling endosomes to melanosomes. Although several Rab GTPases have been shown to regulate these trafficking steps, the precise role of Rab9A remains unknown. Here, we found that a cohort of Rab9A associates with the melanosomes and its knockdown in melanocytes results in hypopigmented melanosomes due to mistargeting of melanosomal proteins to lysosomes. In addition, the Rab9A‐depletion phenotype resembles Rab38/32‐inactivated or BLOC‐3‐deficient melanocytes, suggesting that Rab9A works in line with BLOC‐3 and Rab38/32 during melanosome cargo transport. Furthermore, silencing of Rab9A, Rab38/32 or its effector VARP, or BLOC‐3‐deficiency in melanocytes decreased the length of STX13‐positive recycling endosomal tubules and targeted the SNARE to lysosomes. This result indicates a defect in directing recycling endosomal tubules to melanosomes. Thus, Rab9A and its co‐regulatory GTPases control STX13‐mediated cargo delivery to maturing melanosomes.
Evolutionary history of Apocheima cinerarius (Lepidoptera: Geometridae), a female flightless moth in northern China
Authors: Liu Shuxian , Jiang Nan , Xue Dayong , Cheng Rui , Qu Yanhua , Li Xinxin , Lei Fumin , Han Hongxiang 
Published: November 2015

The alterations in the phylogeographical structures of insects in response to the uplift of the Qinghai–Tibet Plateau and the Quaternary glaciations in eastern Asia, particularly in northern China, remain largely unknown. In this study, we selected Apocheima cinerarius, a moth with flightless females, using molecular data (complete mitochondrial genomes and nuclear data) and ecological niche modelling (ENM) to investigate the effects of paleoclimatic changes on the evolutionary history of insects in the area of northern China. The phylogenetic tree of complete mitochondrial genomes indicated that there were two lineages, the western and eastern lineages. The nuclear gene analyses also detected unique haplotypes in each lineage. Time of the most recent common ancestor (TMRCA) of the two lineages was approximately in Early–Middle Pleistocene. Bayesian skyline plots revealed that the western lineage underwent a population expansion event after the Last Glacial Maximum, whereas the eastern lineage underwent expansion between the Last Interglacial and the Last Glacial Maximum. Our results suggest that A. cinerarius expanded eastward from western sites until the moth was distributed across the entire region of northern China. Then, A. cinerarius underwent contraction into isolated glacial refugia followed by subsequent expansion driven by Pleistocene climate changes, which established a narrow sympatric area. Our results indicate that the Quaternary environmental fluctuations had profound influences on the diversification and demography of an insect in northern China, and the same species in north‐western China and north‐eastern China have different demographic histories.
Role of Non-Active-Site Residue Trp-93 in the Function and Stability of New Delhi Metallo-β-Lactamase 1
Authors: Khan Asad U. , Rehman M. Tabish 
Published: November 2015

ABSTRACT

New Delhi metallo-β-lactamase-1 (NDM-1) is expressed by various members of
Enterobacteriaceae
as a defense mechanism to hydrolyze β-lactam antibiotics. Despite various studies showing the significance of active-site residues in the catalytic mechanism, there is a paucity of reports addressing the role of non-active-site residues in the structure and function of NDM-1. In this study, we investigated the significance of non-active-site residue Trp-93 in the structure and function of NDM-1. We cloned
bla
NDM-1
from an
Enterobacter cloacae
clinical strain (EC-15) and introduced the mutation of Trp-93 to Ala (yielding the Trp93Ala mutant) by PCR-based site-directed mutagenesis. Proteins were expressed and purified to homogeneity by affinity chromatography. The MICs of the Trp93Ala mutant were reduced 4- to 8-fold for ampicillin, cefotaxime, ceftazidime, cefoxitin, imipenem, and meropenem. The poor hydrolytic activity of the Trp93Ala mutant was also reflected by its reduced catalytic efficiency. The overall catalytic efficiency of the Trp93Ala mutant was reduced by 40 to 55% (the

K
m

was reduced, while the
k
cat
was similar to that of wild-type NDM-1 [wtNDM-1]). Heat-induced denaturation showed that the Δ
G
D
o
and

T
m

of Trp93Ala mutant were reduced by 1.8 kcal/mol and 4.8°C, respectively. Far-UV circular dichroism (CD) analysis showed that the α-helical content of the Trp93Ala mutant was reduced by 2.9%. The decrease in stability and catalytic efficiency of the Trp93Ala mutant was due to the loss of two hydrogen bonds with Ser-63 and Val-73 and hydrophobic interactions with Leu-65, Val-73, Gln-123, and Asp-124. The study provided insight into the role of non-active-site amino acid residues in the hydrolytic mechanism of NDM-1.
Acquired Flucytosine Resistance during Combination Therapy with Caspofungin and Flucytosine for Candida glabrata Cystitis
Authors: Charlier Caroline , El Sissy Carine , Bachelier-Bassi Sophie , Scemla Anne , Quesne Gilles , Sitterlé Emilie , Legendre Christophe , Lortholary Olivier , Bougnoux Marie-Elisabeth 
Published: November 2015

ABSTRACTTreatment ofCandida glabratacystitis remains a therapeutic challenge, and an antifungal combination using flucytosine is one option. We describe two patients with refractoryC. glabratacystitis who failed flucytosine combined with caspofungin with early-acquired high-level resistance to flucytosine due to nonsense mutations in theFUR1gene. Rapidly acquired flucytosine resistance with microbiological failure should discourage combination of caspofungin and flucytosine during urinary candidiasis.
Incompatible Natures of the HIV-1 Envelope in Resistance to the CCR5 Antagonist Cenicriviroc and to Neutralizing Antibodies
Authors: Kuwata Takeo , Enomoto Ikumi , Baba Masanori , Matsushita Shuzo 
Published: November 2015

ABSTRACT

Cenicriviroc is a CCR5 antagonist which prevents human immunodeficiency virus type 1 (HIV-1) from cellular entry. The CCR5-binding regions of the HIV-1 envelope glycoprotein are important targets for neutralizing antibodies (NAbs), and mutations conferring cenicriviroc resistance may therefore affect sensitivity to NAbs. Here, we used the
in vitro
induction of HIV-1 variants resistant to cenicriviroc or NAbs to examine the relationship between resistance to cenicriviroc and resistance to NAbs. The cenicriviroc-resistant variant KK
652-67
(strain KK passaged 67 times in the presence of increasing concentrations of cenicriviroc) was sensitive to neutralization by NAbs against the V3 loop, the CD4-induced (CD4i) region, and the CD4-binding site (CD4bs), whereas the wild-type (WT) parental HIV-1 strain KK
WT
from which cenicriviroc-resistant strain KK
652-67
was obtained was resistant to these NAbs. The V3 region of KK
652-67
was important for cenicriviroc resistance and critical to the high sensitivity of the V3, CD4i, and CD4bs epitopes to NAbs. Moreover, induction of variants resistant to anti-V3 NAb 0.5γ and anti-CD4i NAb 4E9C from cenicriviroc-resistant strain KK
652-67
resulted in reversion to the cenicriviroc-sensitive phenotype comparable to that of the parental strain, KK
WT
. Resistance to 0.5γ and 4E9C was caused by the novel substitutions R315K, G324R, and E381K in the V3 and C3 regions near the substitutions conferring cenicriviroc resistance. Importantly, these amino acid changes in the CCR5-binding region were also responsible for reversion to the cenicriviroc-sensitive phenotype. These results suggest the presence of key amino acid residues where resistance to cenicriviroc is incompatible with resistance to NAbs. This implies that cenicriviroc and neutralizing antibodies may restrict the emergence of variants resistant to each other.
Identification and Characterization of a New 7-Aminocephalosporanic Acid Deacetylase from Thermophilic Bacterium Alicyclobacillus tengchongensis
Authors: Ding Jun-Mei , Yu Ting-Ting , Han Nan-Yu , Yu Jia-Lin , Li Jun-Jun , Yang Yun-Juan , Tang Xiang-Hua , Xu Bo , Zhou Jun-Pei , Tang Hong-Zhi , Huang Zun-Xi 
Published: November 2015

ABSTRACTDeacetylation of 7-aminocephalosporanic acid (7-ACA) at position C-3 provides valuable starting material for producing semisynthetic β-lactam antibiotics. However, few enzymes have been characterized in this process before now. Comparative analysis of the genome of the thermophilic bacteriumAlicyclobacillus tengchongensisrevealed a hypothetical protein (EstD1) with typical esterase features. The EstD1 protein was functionally cloned, expressed, and purified fromEscherichia coliBL21(DE3). It indeed displayed esterase activity, with optimal activity at around 65°C and pH 8.5, with a preference for esters with short-chain acyl esters (C2to C4). Sequence alignment revealed that EstD1 is an SGNH hydrolase with the putative catalytic triad Ser15, Asp191, and His194, which belongs to carbohydrate esterase family 12. EstD1 can hydrolyze acetate at the C-3 position of 7-aminocephalosporanic acid (7-ACA) to form deacetyl-7-ACA, which is an important starting material for producing semisynthetic β-lactam antibiotics. EstD1 retained more than 50% of its initial activity when incubated at pH values ranging from 4 to 11 at 65°C for 1 h. To the best of our knowledge, this enzyme is a new SGNH hydrolase identified from thermophiles that is able to hydrolyze 7-ACA.IMPORTANCEDeacetyl cephalosporins are highly valuable building blocks for the industrial production of various kinds of semisynthetic β-lactam antibiotics. These compounds are derived mainly from 7-ACA, which is obtained by chemical or enzymatic processes from cephalosporin C. Enzymatic transformation of 7-ACA is the main method because of the adverse effects chemical deacylation brought to the environment. SGNH hydrolases are widely distributed in plants. However, the tools for identifying and characterizing SGNH hydrolases from bacteria, especially from thermophiles, are rather limited. Here, our work demonstrates that EstD1 belongs to the SGNH family and can hydrolyze acetate at the C-3 position of 7-ACA. Moreover, this study can enrich our understanding of the functions of these enzymes from this family.
Regulation of Chlamydia Gene Expression by Tandem Promoters with Different Temporal Patterns
Authors: Rosario Christopher J. , Tan Ming 
Published: November 2015

ABSTRACT

Chlamydia
is a genus of pathogenic bacteria with an unusual intracellular developmental cycle marked by temporal waves of gene expression. The three main temporal groups of chlamydial genes are proposed to be controlled by separate mechanisms of transcriptional regulation. However, we have noted genes with discrepancies, such as the early gene
dnaK
and the midcycle genes
bioY
and
pgk
, which have promoters controlled by the late transcriptional regulators EUO and σ
28
. To resolve this issue, we analyzed the promoters of these three genes
in vitro
and in
Chlamydia trachomatis
bacteria grown in cell culture. Transcripts from the σ
28
-dependent promoter of each gene were detected only at late times in the intracellular infection, bolstering the role of σ
28
RNA polymerase in late gene expression. In each case, however, expression prior to late times was due to a second promoter that was transcribed by σ
66
RNA polymerase, which is the major form of chlamydial polymerase. These results demonstrate that chlamydial genes can be transcribed from tandem promoters with different temporal profiles, leading to a composite expression pattern that differs from the expression profile of a single promoter. In addition, tandem promoters allow a gene to be regulated by multiple mechanisms of transcriptional regulation, such as DNA supercoiling or late regulation by EUO and σ
28
. We discuss how tandem promoters broaden the repertoire of temporal gene expression patterns in the chlamydial developmental cycle and can be used to fine-tune the expression of specific genes.

IMPORTANCE
Chlamydia
is a pathogenic bacterium that is responsible for the majority of infectious disease cases reported to the CDC each year. It causes an intracellular infection that is characterized by coordinated expression of chlamydial genes in temporal waves. Chlamydial transcription has been shown to be regulated by DNA supercoiling, alternative forms of RNA polymerase, and transcription factors, but the number of transcription factors found in
Chlamydia
is far fewer than the number found in most bacteria. This report describes the use of tandem promoters that allow the temporal expression of a gene or operon to be controlled by more than one regulatory mechanism. This combinatorial strategy expands the range of expression patterns that are available to regulate chlamydial genes.
Prevalence and temporal pattern of hospital readmissions for patients with type I and type II diabetes
Authors: Liu Xiaoqian , Liu Yuanyuan , Lv Yuanjun , Li Changping , Cui Zhuang , Ma Jun 
Published: November 2015

ObjectiveRepeated hospitalisation for patients is common and costly, yet partly preventable. However, we know little about readmissions for patients with diabetes in China. The current study aims to assess the frequency and temporal pattern of and risk factors for all-cause readmission among hospitalised patients with diabetes in Tianjin, China.MethodThis retrospective, cohort analysis used the Tianjin Basic Medical Insurance Register System data of 2011. The patterns of and the reasons for all-cause readmissions for patients with diabetes were described. The differences of readmission-free survival (RFS) between newly and previously diagnosed patients were compared. Time-dependent Cox models were established to identify the risk factors for readmission at different time intervals after discharge.ResultsReadmission rates were approximately 30%, with the most common diagnoses of cerebral infarction (for type I) or diabetes (for type II) for patients with diabetes. The majority of patients were readmitted to the hospital after more than 90 days, followed by 8–30 days (all p=0.002). Approximately 37.2% and 42.8% of readmitted patients with type I and type II diabetes were diagnosed previously, and the RFS rates for previously diagnosed patients were significantly lower than for newly diagnosed patients at any time interval after discharge. Prior history of diabetes (all p<0.05), length of stay (all p<0.01) and reimbursement ratio (90% vs >92%, all p<0.0002) were consistently associated with the RFS for patients readmitted to the hospital at <7, 8–30, 31–60 and 61–90 days.ConclusionsHospital readmissions among patients with diabetes were affected by the diagnosis status. Patient characteristics and the quality of healthcare might regulate short-interval and long-interval hospital readmission, respectively, after discharge.
Bicycling injury hospitalisation rates in Canadian jurisdictions: analyses examining associations with helmet legislation and mode share
Authors: Teschke Kay , Koehoorn Mieke , Shen Hui , Dennis Jessica 
Published: November 2015

ObjectivesThe purpose of this study was to calculate exposure-based bicycling hospitalisation rates in Canadian jurisdictions with different helmet legislation and bicycling mode shares, and to examine whether the rates were related to these differences.MethodsAdministrative data on hospital stays for bicycling injuries to 10 body region groups and national survey data on bicycling trips were used to calculate hospitalisation rates. Rates were calculated for 44 sex, age and jurisdiction strata for all injury causes and 22 age and jurisdiction strata for traffic-related injury causes. Inferential analyses examined associations between hospitalisation rates and sex, age group, helmet legislation and bicycling mode share.ResultsIn Canada, over the study period 2006–2011, there was an average of 3690 hospitalisations per year and an estimated 593 million annual trips by bicycle among people 12 years of age and older, for a cycling hospitalisation rate of 622 per 100 million trips (95% CI 611 to 633). Hospitalisation rates varied substantially across the jurisdiction, age and sex strata, but only two characteristics explained this variability. For all injury causes, sex was associated with hospitalisation rates; females had rates consistently lower than males. For traffic-related injury causes, higher cycling mode share was consistently associated with lower hospitalisation rates. Helmet legislation was not associated with hospitalisation rates for brain, head, scalp, skull, face or neck injuries.ConclusionsThese results suggest that transportation and health policymakers who aim to reduce bicycling injury rates in the population should focus on factors related to increased cycling mode share and female cycling choices. Bicycling routes designed to be physically separated from traffic or along quiet streets fit both these criteria and are associated with lower relative risks of injury.