bluuebunny/crossref_metadata_2025_split huggingface dataset:
CIN‐TCP transcription factors: Transiting cell proliferation in plants
Authors: Sarvepalli Kavitha , Nath Utpal 
Published: June 2018

AbstractLeaves are the most conspicuous planar organs in plants, designed for efficient capture of sunlight and its conversion to energy that is channeled into sustaining the entire biosphere. How a few founder cells derived from the shoot apical meristem give rise to diverse leaf forms has interested naturalists and developmental biologists alike. At the heart of leaf morphogenesis lie two simple cellular processes, division and expansion, that are spatially and temporally segregated in a developing leaf. In leaves of dicot model species, cell division occurs predominantly at the base, concomitant with the expansion and differentiation of cells at the tip of the lamina that drives increase in leaf surface area. The timing of the transition from one cell fate (division) to the other (expansion) within a growing leaf lamina is a critical determinant of final leaf shape, size, complexity and flatness. The TCP proteins, unique to plant kingdom, are sequence‐specific DNA‐binding transcription factors that control several developmental and physiological traits. A sub‐group of class II TCPs, called CINCINNATA‐like TCPs (CIN‐TCPs henceforth), are key regulators of the timing of the transition from division to expansion in dicot leaves. The current review highlights recent advances in our understanding of how the pattern of CIN‐TCP activity is translated to the dynamic spatio‐temporal control of cell‐fate transition through the transactivation of cell‐cycle regulators, growth‐repressing microRNAs, and interactions with the chromatin remodeling machinery to modulate phytohormone responses. Unravelling how environmental inputs influence CIN‐TCP‐mediated growth control is a challenge for future studies. © 2018 IUBMB Life, 70(8):718–731, 2018
Have we realized the full potential of β‐lactams for treating drug‐resistant TB?
Authors: Story‐Roller Elizabeth , Lamichhane Gyanu 
Published: June 2018

Abstractβ‐lactams are the most widely used antibiotics and are effective against a spectrum of pathogenic bacteria. Here, we focus on the state‐of‐the‐art understanding of the molecular underpinnings that determine the overall efficacy of β‐lactams against TB and include historical perspectives of this antibiotic class against this ancient disease. We summarize literature that describes why earlier generations of β‐lactams are ineffective and the potential promise of newer β‐lactams that exhibit improved efficacy against TB. Emerging evidence warrants renewed consideration of newer β‐lactams in regimens for treatment of drug‐resistant TB. © 2018 IUBMB Life, 70(9):881–888, 2018
Genetic association between SHANK2 polymorphisms and susceptibility to autism spectrum disorder
Authors: Bai Ye , Qiu Shuang , Li Yan , Li Yong , Zhong Weijing , Shi Meijuan , Zhu Xiaojuan , Jiang Huiyi , Yu Yaqin , Cheng Yi , Liu Yawen 
Published: June 2018

AbstractAutism spectrum disorder (ASD), as one of early‐onset neurodevelopmental disorders, is characterized by the following symptoms, including repetitive and stereotyped behaviors, impairments in social interaction, and dysfunctions in communication. ASD afflicts ∼1.5% of children aged 8 years in America and ∼4.5‰ of children aged 0–6 years in China. Existing studies suggest that SH3 and multiple ankyrin repeat domains protein 2 (SHANK2) is implicated in ASD. However, associations between SNPs in SHANK2 introns and ASD risk have been less investigated. In this study, on the basis of case‐control study (226 cases and 239 controls), we selected nine SNPs (rs76717360, rs11236697, rs74336682, rs77950809, rs17428526, rs35459123, rs75357229, rs61887413, and rs77716438) in SHANK2 introns to investigate genetic associations between SHANK2 polymorphisms and susceptibility to ASD using improved multiple ligase detection reaction (iMLDR). We identified that the polymorphism of rs76717360 was associated with risk of ASD in Chinese population; the haplotype of rs11236697 C (T) or rs74336682 G (A) increased ASD risk; and haplotypes with ≥ five SNPs containing rs11236697 and rs74336682 were associated with risk of ASD. Our results indicate SHANK2 is a susceptibility gene for ASD in Chinese children. © 2018 IUBMB Life, 70(8):763–776, 2018
Genome wide analysis of meiotic recombination in yeast: For a few SNPs more
Authors: Chakraborty Parijat , Pankajam Ajith V. , Dutta Abhishek , Nishant Koodali T. 
Published: June 2018

AbstractDiploid organisms undergo meiosis to produce haploid germ cells. Crossover events during meiosis promote genetic diversity and facilitate accurate chromosome segregation. The baker's yeast Saccharomyces cerevisiae is extensively used as a model for analysis of meiotic recombination. Conventional methods for measuring recombination events in S. cerevisiae have been limited by the number and density of genetic markers. Next generation sequencing (NGS)‐based analysis of hybrid yeast genomes bearing thousands of heterozygous single nucleotide polymorphism (SNP) markers has revolutionized analysis of meiotic recombination. By facilitating analysis of marker segregation in the whole genome with unprecedented resolution, this method has resulted in the generation of high‐resolution recombination maps in wild‐type and meiotic mutants. These studies have provided novel insights into the mechanism of meiotic recombination. In this review, we discuss the methodology, challenges, insights and future prospects of using NGS‐based methods for whole genome analysis of meiotic recombination. The objective is to facilitate the use of these high through‐put sequencing methods for the analysis of meiotic recombination given their power to provide significant new insights into the process. © 2018 The Authors. IUBMB Life published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 70(8):743–752, 2018
Centromere and its associated proteins—what we know about them in Plasmodium falciparum
Authors: Verma Garima , Surolia Namita 
Published: June 2018

AbstractThe complex life cycle of intracellular parasitic protozoans entails multiple rounds of DNA replication and mitosis followed by cytokinesis to release daughter parasites. To gain insights into mitotic events it is imperative to identify the biomarkers that constitute the chromosome segregation machinery in the parasite. Chromosomal loci called centromeres and their associated proteins play an essential role in accurate chromosome segregation. Although new information on the centromere‐kinetochore proteins has been added to the existing pool of knowledge, a paucity of biomarkers for nuclear division prevents a global view of chromosome segregation mechanism in the malaria parasite. In Plasmodium falciparum, except CENH3 and CENP‐C homologues, other centromere associated proteins responsible for centromere functions and kinetochore assembly are not known. The focus of this review is to summarize the current understanding on the centromere organization and its associated proteins in eukaryotes with the emerging information in P. falciparum. © 2018 IUBMB Life, 70(8):732–742, 2018
Efficacy and safety of a clinically relevant foamy vector design in human hematopoietic repopulating cells
Authors: Everson Elizabeth M. , Hocum Jonah D. , Trobridge Grant D. 
Published: June 2018

AbstractBackgroundPrevious studies have shown that foamy viral (FV) vectors are a promising alternative to gammaretroviral and lentiviral vectors and also that insulators can improve FV vector safety. However, in a previous analysis of insulator effects on FV vector safety, strong viral promoters were used to elicit genotoxic events. In the present study, we developed and analyzed the efficacy and safety of a high‐titer, clinically relevant FV vector driven by the housekeeping promoter elongation factor‐1α and insulated with an enhancer blocking A1 insulator (FV‐EGW‐A1).MethodsHuman CD34+ cord blood cells were exposed to an enhanced green fluorescent protein expressing vector, FV‐EGW‐A1, at a multiplicity of infection of 10 and then maintained in vitro or transplanted into immunodeficient mice. Flow cytometry was used to measure engraftment and marking in vivo. FV vector integration sites were analyzed to assess safety.ResultsFV‐EGW‐A1 resulted in high‐marking, multilineage engraftment of human repopulating cells with no evidence of silencing. Engraftment was highly polyclonal with no clonal dominance and a promising safety profile based on integration site analysis.ConclusionsAn FV vector with an elongation factor‐1α promoter and an A1 insulator is a promising vector design for use in the clinic.
Elucidating the mass spectrum of the retronecine alkaloid using DFT calculations
Authors: Modesto‐Costa Lucas , Martinez Sabrina T. , Pinto Angelo C. , Vessecchi Ricardo , Borges Itamar 
Published: June 2018

AbstractPyrrolizidine alkaloids are natural molecules playing important roles in different biochemical processes in nature and in humans. In this work, the electron ionization mass spectrum of retronecine, an alkaloid molecule found in plants, was investigated computationally. Its mass spectrum can be characterized by three main fragment ions having the following m/z ratios: 111, 94, and 80. In order to rationalize the mass spectrum, minima and transition state geometries were computed using density functional theory. It was showed that the dissociation process includes an aromatization of the originally five‐membered ring of retronecine converted into a six‐membered ring compound. A fragmentation pathway mechanism involving dissociation activation barriers that are easily overcome by the initial ionization energy was found. From the computed quantum chemical geometric, atomic charges, and energetic parameters, the abundance of each ion in the mass spectrum of retronecine was discussed.
Accelerated reactions in field desorption mass spectrometry
Authors: Chen Xingshuo , Cooks R. Graham 
Published: June 2018

AbstractField desorption mass spectrometry under ambient conditions is used to study solution‐phase organic reactions in micro‐volumes. Reagent solution is transferred onto the microdendrites of the field emitter, and reaction products are examined online by mass spectrometry. Three reactions, hydrazone formation by phenyl hydrazine and indoline‐2,3‐dione, the Katritzky reaction between a pyrylium salt and anisidine, and the Hantzsch synthesis of 1,4‐dihydropyridine, were investigated, and reaction acceleration was observed to different extents. The increase in rate relative to the corresponding bulk reactions is attributed to solvent evaporation (simple concentration effect) and to the increase of surface‐to‐volume ratio (enhanced interfacial reactions). A distinguishing feature of this method of reaction acceleration, relative to that based on nano electrospray ionization, is the observation of radical cations and the formation of radical cation products. The study also breaks new ground in using field emitters at atmospheric pressure.
The hypolipidemic effects of peptides prepared from Cicer arietinum in ovariectomized rats and HepG2 cells
Authors: Shi Wen , Hou Tao , Liu Weiwei , Guo Danjun , He Hui 
Published: June 2018

AbstractBACKGROUNDThe lack of estrogen in postmenopausal women is a key risk factor for disorders of lipid metabolism and for obesity. Except in cases where estrogen replacement therapy (ERT) is being used, chickpea peptides (ChPs) may be a potential candidate for treating hyperlipidemia.RESULTSIn ovariectomized rats model, ChPs were found to decrease body weight, adipose tissue size, total cholesterol (TC), total triglyceride (TG), low‐density lipoprotein cholesterol (LDL‐C), and the atherogenic index (AI) in serum and liver TC and TG. Serum high‐density lipoprotein cholesterol (HDL‐C), bile acids in liver and feces, fecal TC and TG were observed to increase significantly (P < 0.05). ChPs play a role in inhibiting the activities of fatty acid synthetase (FAS) and HMG‐CoA reductase (HMGR). The expression of peroxisome proliferator‐activated receptors (PPAR)γ and sterol regulatory element‐binding protein (SREBP)‐1c were downregulated and the expression of liver X receptor (LXR) α, estrogen receptor(ER)α and ERβ were upregulated by ChPs. In HepG2 cell experiments, the cellular TC levels decreased and the uptake of NBD‐cholesterol increased significantly after treatment with Mw < 1 kDa and Mw < 5 kDa ChPs fractions. Val‐Phe‐Val‐Arg‐Asn (VFVRN) could inhibit TC biosynthesis by decreasing the expression of HMGR.CONCLUSIONWe demonstrated that ChPs could effectively regulate lipid metabolism disorders and restrain obesity caused by estrogen deficiency. Val‐Phe‐Val‐Arg‐Asn identified from ChPs could reduce the expression of HMGR to inhibit cholesterol biosynthesis. © 2018 Society of Chemical Industry
Tgfbr2 is required in Acan‐expressing cells for maintenance of the intervertebral and sternocostal joints
Authors: Alkhatib Bashar , Liu Cunren , Serra Rosa 
Published: June 2018

BackgroundMembers of the transforming growth factor beta (TGF‐β) family are secreted proteins that regulate skeletal development. TGF‐β signaling is critical in embryonic development of the annulus fibrosus (AF) of the intervertebral disc (IVD). To address the question of the role of TGF‐β signaling in postnatal development and maintenance of the skeleton, we generated mice in which Tgfbr2 was deleted at 2‐weeks of age in Aggrecan (Acan)‐expressing cells using inducible Cre/LoxP recombination.MethodsLocalization of Cre recombination was visualized by crossing Acantm1(cre/ERT2)Crm mice to fluorescent mTmG reporter mice. Acantm1(cre/ERT2)Crm mice were mated to Tgfbr2LoxP/LoxP mice and Cre recombinase was activated by tamoxifen injection at 2‐weeks postnatally. Following tamoxifen injection, mice were aged to 3, 6, and 12‐months and control mice were compared to the experimental (cKO) group. Mice were initially analyzed using X‐ray and skeletal preparations. Sternocostal joints and IVD tissues were further analyzed histologically by hematoxylin and eosin (H&E), Safranin O, and Picrosirius Red staining as well as Col10 immunostaining.ResultsCre recombination was observed in the IVD and sternocostal joints. X‐ray analysis revealed osteophyte formation within the disc space of 12‐month‐old cKO mice. Skeletal preparations confirmed calcification within the IVD and the sternocostal joints in cKO mice. H&E staining of cKO IVD revealed disorganized growth plates, delay in the formation of the bony endplate, and Col10 staining in the AF indicative of ectopic endochondral bone formation. Furthermore, proteoglycan loss was observed and collagen bundles within the inner AF were thinner and less organized. Alterations in the IVD were apparent beginning at 3 months and were progressively more visible at 6 and 12 months. Similarly, histological analysis of cKO sternocostal joints revealed joint calcification, proteoglycan loss, and disorganization of the collagen architecture at 12 months of age.ConclusionsTGF‐β signaling is important for postnatal development and maintenance of fibrocartilaginous IVD and sternocostal joints.
Urinary l‐kynurenine quantification and selective extraction through a molecularly imprinted solid‐phase extraction device
Authors: Mergola Lucia , Orabona Ciriana , Albini Elisa , Vasapollo Giuseppe , Scorrano Sonia , Del Sole Roberta 
Published: June 2018

Abstractl‐Kynurenine is an endogenous metabolite generated by the catabolic pathway of l‐tryptophan and it could be a potential biomarker to test the efficacy of several checkpoint inhibitors that have already reached the clinical trials in the antitumor therapy. Thus, a molecularly imprinted polymer specific for the recognition of this metabolite was synthesized and used as innovative system in solid‐phase extraction technique for the specific extraction and quantification of l‐kynurenine in human urine. The off‐line system was firstly tested on l‐kynurenine standard solutions, allowing recoveries up to 97.7% (relative standard deviation = 2.2%) and then applied to fortified and deproteinated human urine samples, where a recovery of 84.1% (relative standard deviation = 3.1%) was obtained. The method was validated and it revealed a good linearity in the range of 0.157–20 μg/mL (r2 = 0.9992). The optimized procedure demonstrated a good feasibility on biological samples, allowing a ready quantification of l‐kynurenine in the human urine, where the metabolite was found at a very low concentration (0.80 μg/mL). The extraction system developed could attract attention of pharmaceutical industries for l‐kynurenine production as potential drug in the treatment of autoimmune disorders through its extraction and purification from biological matrixes.
Comparing yield and growth characteristics of four pastoral plant species under two salinity soil levels
Authors: Tlili Abderrazak , Tarhouni Mohamed , Cerdà Artemi , Louhaichi Mounir , Neffati Mohamed 
Published: June 2018

AbstractThe vegetation cover and the biomass production of the rangeland ecosystems are decreasing at an alarming rate. The valorization of saline water, by irrigating planted pastoral halophytes on salt‐affected soils, is considered among the valuable tools to increase their production. In this study, the ability of four plant species (Atriplex halimus L. [Amaranthaceae], Atriplex mollis Desf. [Amaranthaceae], Lotus creticus L. [Fabaceae], and Cenchrus ciliaris L. [Poaceae]) to grow is tested in two field plots—low (low salinity plot [LSP]) and high (high salinity plot [HSP]) soil salinity. Canopy cover, dry biomass, and some chemical analyses (ash, nitrogen, and polyphenol contents) are undertaken. Main results show that A. halimus is the most able to grow in the two plots because it shows the greatest covers during the experiment. The covers of others species are low both in LSP and HSP. A. mollis retains the highest dry matter in both LSP (157 and 236 g) and HSP (134 and 153 g) when cutting 1/2 and 2/3 of the aboveground biomass, respectively. A. halimus and A. mollis have the biggest ash content in both LSP (respectively 65 and 67.5 mg g−1 fresh matter) and HSP (112.5 and 100 mg g−1 fresh matter). L. creticus and A. halimus show the highest total nitrogen content in LSP (respectively 26.9 and 26.3 g kg−1 dry matter). All the species reduced their nitrogen in HSP despite the C. ciliaris content that remains constant. In conclusion, the ability of the retained species to grow under high soil salinity is noted. Hence, the saline soils can be rehabilitated by planting well‐targeted pastoral halophytes.
Effect of long‐term application of manure and nitrogen fertilizer on infiltration for a wheat–maize rotation system
Authors: Liu Shutang , Zhang Hanyu , Liu Qianjin , Zong Hui , Yu Xingxiu 
Published: June 2018

AbstractModelling soil infiltration capacity and identifying controlling factors under long‐term fertilizer application could help in developing better fertilization treatments to increase infiltration, thereby preventing land degradation. This study was performed at Laiyang long‐term fertilization experimental field in Shandong Province, China. Three application rates of manure (0, 30,000, and 60,000 kg ha−2) and nitrogen (0, 138, and 276 kg ha−2) were full designed in a nine‐treatment randomized block design with three replicates per treatment. The infiltration processes were detected using an automatic infiltration measurement system and represented by three indices, that is, initial infiltration rate for the first 3 min (Ii), the average infiltration rate for the whole 30‐min period (Ia), and the final infiltration rate for the last 3 min (If). Manure application could increaseIaandIfsignificantly (p < 0.01). Nitrogen application had no significant effect on infiltration. The linkage between potential influencing factors and infiltration capacity indices was analysed by partial least squares regression (PLSR), an efficient method that can deal with high colinear variables. The optimal PLSR model could explain 95% of the variability in potential influencing factors and 92% of the variability in soil infiltration capacity indices and could predict 82% of the variability in soil infiltration capacity. Three soil properties, that is, organic matter content, bulk density, and weight ratio of soil aggregate with diameter greater than 0.25 mm measured using wet sieving method, were identified as main influencing factors. The results would be informative to assess infiltration and then land degradation after a long‐term cultivation.
An assessment of the variation of soil properties with landscape attributes in the highlands of Cameroon
Authors: Takoutsing Bertin , Weber John C. , Rodríguez Martín Jose Antonio , Shepherd Keith , Aynekulu Ermias , Sila Andrew 
Published: June 2018

AbstractSoil properties are useful for assessing the potential of landscapes to provide terrestrial ecosystem services, but they are affected by anthropogenic activities and environmental factors including landscape attributes. This study assessed how soil properties are influenced by landscape attributes and their interactions in the highlands of Cameroon using the Land Degradation Surveillance Framework as a data collection tool. Soil properties (soil organic carbon [SOC], clay content, exchangeable bases [ExBas], electric conductivity [EC], boron [B], manganese [Mn], phosphorus [P], pH) were quantified within classes of landscape attributes. Soil samples were collected on 160 (1,000 m2) plots randomly located in a sentinel site of 100 km2 and were analyzed using a combination of conventional laboratory methods and mid‐infrared spectroscopy. Soil properties were highly affected by soil depths, land use types, slope gradients, and topographic positions, but less by their interactions. Significant interactions existed between land use types and topographic positions for SOC, EC, ExBas, and pH, and between slope gradients and topographic positions for pH, whereas Mn was influenced by the interaction between land use types and slope gradients. Most soil properties were higher in low altitude plots and those with higher vegetation cover but decreased in the upslope direction. The pH and clay contents were less affected by slope gradient confirming the inherent nature of the properties. These results are useful for site‐specific implementation of ecological intensification in areas with complex topography such as the highlands of Cameroon, offering a reference for future ecological policies and landscape restoration.