bluuebunny/crossref_metadata_2025 huggingface dataset:
Prediction and identification of natural antisense transcripts and their small RNAs in soybean (Glycine max)
Authors: Zheng Hu , Qiyan Jiang , Zhiyong Ni , Hui Zhang
Published: April 2013

Background

Natural antisense transcripts (NATs) are a class of RNAs that contain a sequence complementary to other transcripts. NATs occur widely in eukaryotes and play critical roles in post-transcriptional regulation. Soybean NAT sequences are predicted in the PlantNATsDB, but detailed analyses of these NATs remain to be performed.

Results

A total of 26,216 NATs, including 994 cis-NATs and 25,222 trans-NATs, were predicted in soybean. Each sense transcript had 1–177 antisense transcripts. We identified 21 trans-NATs using RT-PCR amplification. Additionally, we identified 179 cis-NATs and 6,629 trans-NATs that gave rise to small RNAs; these were enriched in the NAT overlapping region. The most abundant small RNAs were 21, 22, and 24 nt in length. The generation of small RNAs was biased to one stand of the NATs, and the degradation of NATs was biased. High-throughput sequencing of the degradome allowed for the global identification of NAT small interfering RNAs (nat-siRNAs) targets. 446 target genes for 165 of these nat-siRNAs were identified. The nat-siRNA target could be one transcript of a given NAT, or from other gene transcripts. We identified five NAT transcripts containing a hairpin structure that is characteristic of pre-miRNA. We identified a total of 86 microRNA (miRNA) targets that had antisense transcripts in soybean.

Conclusions

We globally identified nat-siRNAs, and the targets of nat-siRNAs in soybean. It is likely that the cis-NATs, trans-NATs, nat-siRNAs, miRNAs, and miRNA targets form complex regulatory networks.
Cortical mapping of the infraspinatus muscle in healthy individuals
Authors: Ngomo Suzy , Mercier Catherine , Roy Jean-Sébastien
Published: April 2013

Background

While cortical representations of intrinsic hand muscles have been extensively studied in healthy individuals, little is known about the representation of proximal upper limb muscles. Improving our understanding of normal shoulder function is important, given that shoulder musculoskeletal disorders affect approximately 20% of the population and are suspected to involve changes in central motor representations. The purpose of the study is to describe the motor representation (motor evoked potentials (MEP) amplitude at the hotspot, map area, normalized map volume and center of gravity) of the infraspinatus muscle in healthy individuals, and to explore the potential influence of hand dominance on this representation (i.e. symmetry of the excitability and of the location of motor map between sides), as well as the effect of age and gender on motor excitability.

Results

Fifteen healthy participants took part in this study. No significant asymmetry between sides was observed for motor excitability (p = 0.14), map area (p = 0.73) and normalized map volume (p = 0.34). Moreover, no side x intensity interaction was found (p = 0.54), indicating similar stimulus response properties. No difference between sides was found in the location of infraspinatus motor representation, either in the mediolateral or anteroposterior axis (p > 0.10). Neither age nor gender influenced aMT (p > 0.58) or MEP size (p > 0.61).

Conclusions

As the cortical representation of infraspinatus muscles was found to be symmetric between sides, both in terms of excitability and location, comparisons between the intact and affected side could be performed in clinical studies, regardless of whether the dominant or non-dominant side is affected. The next step will be to characterize corticospinal excitability and map parameters in populations with shoulder disorders.
Eyebrow hairs from actinic keratosis patients harbor the highest number of cutaneous human papillomaviruses
Authors: Schneider Ines , Lehmann Mandy D , Kogosov Vlada , Stockfleth Eggert , Nindl Ingo
Published: April 2013

Background

Cutaneous human papillomavirus (HPV) infections seem to be associated with the onset of actinic keratosis (AK). This study compares the presence of cutaneous HPV types in eyebrow hairs to those in tissues of normal skin and skin lesions of 75 immunocompetent AK patients.

Methods

Biopsies from AK lesions, normal skin and plucked eyebrow hairs were collected from each patient. DNA from these specimens was tested for the presence of 28 cutaneous HPV (betaPV and gammaPV) by a PCR based method.

Results

The highest number of HPV prevalence was detected in 84% of the eyebrow hairs (63/75, median 6 types) compared to 47% of AK lesions (35/75, median 3 types) (p< 0.001) and 37% of normal skin (28/75, median 4 types) (p< 0.001), respectively. A total of 228 HPV infections were found in eyebrow hairs compared to only 92 HPV infections in AK and 69 in normal skin. In all three specimens HPV20, HPV23 and/or HPV37 were the most prevalent types. The highest number of multiple types of HPV positive specimens was found in 76% of the eyebrow hairs compared to 60% in AK and 57% in normal skin. The concordance of at least one HPV type in virus positive specimens was 81% (three specimens) and 88-93% of all three combinations with two specimens.

Conclusions

Thus, eyebrow hairs revealed the highest number of cutaneous HPV infections, are easy to collect and are an appropriate screening tool in order to identify a possible association of HPV and AK.
Cholinergic muscarinic receptor activation augments murine intestinal epithelial cell proliferation and tumorigenesis
Authors: Peng Zhongsheng , Heath Jonathon , Drachenberg Cinthia , Raufman Jean-Pierre , Xie Guofeng
Published: April 2013

Background

Previously, we showed that M3 muscarinic receptor (M3R; gene name Chrm3) deficiency attenuates murine intestinal neoplasia, supporting the hypothesis that muscarinic receptors play an important role in intestinal tumorigenesis.

Methods

To test this hypothesis, in the present study we treated mice with bethanechol, a non-selective muscarinic receptor agonist without nicotinic receptor activity, and examined its effects on azoxymethane (AOM)-induced colon neoplasia. Mice were provided with drinking water containing 400 μg/mL bethanechol chloride or water without additions (control) for a total of 20 weeks, a period that included the initial 6 weeks when mice received intraperitoneal injections of AOM.

Results

When euthanized at week 20, control mice had 8.0 ± 1.3 tumors per animal, whereas bethanechol-treated mice had 10.4 ± 1.5 tumors per mouse (mean ± SE; P = 0.023), a 30% increase. Strikingly, tumor volume per animal was increased 52% in bethanechol-treated compared with control mice (179.7 ± 21.0 vs. 111. 8 ± 22.4 mm3; P = 0.047). On histological examination, bethenechol-treated mice also had more adenocarcinomas per animal (8.0 ± 1.0 vs. 4.1 ± 0.6 for control mice, P = 0.0042). Cell proliferation in both normal mucosa and adenocarcinomas was increased in bethanechol-treated compared to control mice. Also, in tumors, bethanechol treatment increased expression of Chrm3, Egfr and post-Egfr signaling molecules Myc and cyclin D1. Bethanechol treatment increased the thickness of normal colonic mucosa and the expression of selected matrix metalloproteinase (Mmp) genes, including Mmp7, Mmp10 and Mmp13.

Conclusions

These findings support a prominent role for muscarinic receptors in colon neoplasia, and identify post-receptor signaling molecules as potential therapeutic targets.
Dieting status influences associations between dietary patterns and body composition in adolescents: a cross-sectional study
Authors: Howe Anna S , Black Katherine E , Wong Jyh Eiin , Parnell Winsome R , Skidmore Paula ML
Published: April 2013

Background

Associations between food choice and body composition in previous studies of adolescents have been inconsistent. This may be due to the body composition measures used, or these associations may be affected by the dieting status of adolescents. The objective of this study was to investigate the association between dietary patterns and body composition in adolescents, and determine if these associations are moderated by dieting status.

Methods

Information on food consumption and current dieting status was collected, using a web-based survey, in 681 adolescents (mean age 15.8 (SD 0.9) years) from schools in Otago, New Zealand. Non-dieters were defined as those reporting not being on a diet as they were “happy with their weight”. Principal components analysis (PCA) was used to determine dietary patterns. Body mass index (BMI), waist circumference (WC), waist-to-height ratio (WHtR), fat mass index (FMI), and fat-free mass index (FFMI) were examined as outcomes. Generalized estimating equations were used to examine associations between dietary patterns and body composition.

Results

PCA produced three dietary patterns: ‘Treat Foods’, ‘Fruits and Vegetables’, and ‘Basic Foods’. A standard deviation increase in ‘Basic Foods’ was associated with a 3.58% decrease in FMI (95%CI −6.14, -0.94) in the total sample. When separate sex analysis was undertaken significant negative associations were found in boys only, between the ‘Basic Food’ score and WC, WHtR, FMI, and FFMI, while the ‘Fruits and Vegetables’ pattern was negatively associated with FMI. Associations between ‘Treat Foods’ and BMI, WC, and WHtR in non-dieters were positive, while these associations were negative for all other participants.

Conclusions

Significant associations were found between dietary patterns and indices of both central and total adiposity, but not BMI. Therefore using only BMI measures may not be useful in this age group. Since our results were significant for boys and not girls, nutrition messages designed to prevent obesity may be particularly important for adolescent boys. As an interaction between dieting status and ‘Treat Foods’ existed, future studies should also explore the role of dieting when investigating food choice and body composition.
Expression of gamma-aminobutyric acid receptors on neoplastic growth and prediction of prognosis in non-small cell lung cancer
Authors: Zhang Xiaoxue , Zhang Rong , Zheng Yuanjie , Shen Jianfei , Xiao Dakai , Li Jin , Shi Xiaoshun , Huang Liyan , Tang Hailing , Liu Jun , He Jianxing , Zhang Haibo
Published: April 2013

Background

Gamma-aminobutyric acid (GABA) is the main inhibitory neurotransmitter in the adult mammalian brain, but exerts physiologic effects other than that on neurotransmitter in non-neuronal peripheral tissues and organs. GABA may affect cancer growth through activation GABA receptors. We investigated the gene expression of GABA receptors in tissue of non-small cell lung cancers (NSCLC) and non-cancerous tissues, and found that the gene expression of GABA receptor phenotypes was correlated with tumorigenesis and clinical prognosis.

Methods

Sixty-one snap-frozen human samples of NSCLC tissues and paired non-cancerous tissues (5cm away from tumor) were analyzed. Gene expression of GABA receptors was detected by Real-time quantitative PCR (RT-qPCR). Survival times in relation to the expression of GABA receptor phenotypes were analyzed. Human NSCLC cell lines H1299, A549, H520, H460 and human bronchial epithelial cell line BEAS-2B were used to determine the phenotypes of GABA inhibitory effects on cancer cell growth. The effects of exogenous administration of GABA on H1299 cell growth were examined.

Results

The gene expressions were significantly higher in NSCLC tissues than in the paired non-cancerous tissues for GABAA receptor subunit α3 (GABRA3, P = 0.030); for GABAA receptor subunit epsilon (GABRE, P = 0.036); and GABAB receptor subunit 2 (GABBR2, P = 0.005). Kaplan-Meier curves showed that patients with high expression of GABBR2 gene and low expression of GABRA3 gene had a better prognosis (P < 0.05). The administration of GABA resulted in suppressed proliferation of NSCLC cell lines in a dose- and time-dependent manner. The use of the GABA receptor antagonist CGP35348 could reverse the inhibitory effect.

Conclusions

The pattern of GABA receptor gene phenotype expression may be involved in the regulation of tumorigenesis. A high expression of GABBR2 with a low expression of GABRA3 may predict a better outcome. The treatment with GABA attenuates cancer cell growth in vitro. The expression of GABA receptor may be not only promising genetic therapeutic targets but may also serve as valuable prognostic markers for NSCLC.
Assembly of PbTe/Pb-based nanocomposite and photoelectric property
Authors: Zong Zhaocun , Wang Hongxia , Kong Lingmin
Published: April 2013

PbTe/Pb-based nanocomposite was assembled by combining the regular PbTe/Pb nanostructure and the Zn
x
Mn1−x
S nanoparticles; the photoelectric property of the nanocomposite was measured in situ. The results showed that the through current of the nanocomposite had an obvious increase compared to that of the individual PbTe/Pb nanomaterial under the same irradiation conditions. The improvement of photoelectric performance would be attributed to the synergistic effect brought by the incident light and exciting light of the Zn
x
Mn1−x
S nanoparticles. The result implied that the underlying mechanism could be used to improve the performance of nano-optoelectronic devices and the light-use efficiency of solar devices.
ZASC1 knockout mice exhibit an early bone marrow-specific defect in murine leukemia virus replication
Authors: Seidel Shannon , Bruce James , Leblanc Mathias , Lee Kuo-Fen , Fan Hung , Ahlquist Paul , Young John AT
Published: April 2013

Background

ZASC1 is a zinc finger-containing transcription factor that was previously shown to bind to specific DNA binding sites in the Moloney murine leukemia virus (Mo-MuLV) promoter and is required for efficient viral mRNA transcription (J. Virol. 84:7473-7483, 2010).

Methods

To determine whether this cellular factor influences Mo-MuLV replication and viral disease pathogenesis in vivo, we generated a ZASC1 knockout mouse model and completed both early infection and long term disease pathogenesis studies.

Results

Mice lacking ZASC1 were born at the expected Mendelian ratio and showed no obvious physical or behavioral defects. Analysis of bone marrow samples revealed a specific increase in a common myeloid progenitor cell population in ZASC1-deficient mice, a result that is of considerable interest because osteoclasts derived from the myeloid lineage are among the first bone marrow cells infected by Mo-MuLV (J. Virol. 73: 1617-1623, 1999). Indeed, Mo-MuLV infection of neonatal mice revealed that ZASC1 is required for efficient early virus replication in the bone marrow, but not in the thymus or spleen. However, the absence of ZASC1 did not influence the timing of subsequent tumor progression or the types of tumors resulting from virus infection.

Conclusions

These studies have revealed that ZASC1 is important for myeloid cell differentiation in the bone marrow compartment and that this cellular factor is required for efficient Mo-MuLV replication in this tissue at an early time point post-infection.
Diesel exhaust particles modify natural killer cell function and cytokine release
Authors: Müller Loretta , Chehrazi Claire VE , Henderson Michael W , Noah Terry L , Jaspers Ilona
Published: April 2013

Background

Natural killer (NK) cells are an important lymphocyte population in the nasal mucosa and play important roles in linking the innate and the adaptive immune response. Their two main functions are direct cell-mediated cytotoxicity and the release of cytokines. They are important during viral infections and cancer. Due to their location in the nasal mucosa, NK cells are likely exposed to inhaled pollutants, such as diesel exhaust. Whether and how exposure to diesel exhaust particles (DEP) affects NK cell function in the context of viral infections has not been investigated.

Methods

NK cells were isolated from peripheral blood obtained from normal healthy volunteers and subsequently stimulated with the viral mimetic polyinosinic:polycytidylic acid (pI:C), DEP, or pI:C+DEP for 18 hours. NK cells were subsequently analyzed for changes in surface marker expression, cytokine production, gene expression changes, and cytotoxic function using flow cytometry, ELISA, qRT-PCR, and cell-mediated cytotoxicity assay, respectively.

Results

Stimulation of NK cells with pI:C and pI:C+DEP, but not DEP alone, increased the release of IL-1β, IL-2, IL-4, IL-8, IL-10, IL-12p70, IFN-γ and TNF-α. As compared to pI:C alone or pI:C+DEP, the release of IL-1β, IL-8 and TNF-α was significantly lower after DEP stimulation alone. Stimulation with pI:C alone increased the gene and protein expression of granzyme B and perforin, which was completely blunted by adding DEP. Addition of DEP further reduced CD16 expression in pI:C stimulated cells. Similarly, cell-mediated cytotoxicity was significantly reduced by the addition of DEP.

Conclusions

In the context of viral infection, DEP potentially reduces NK cells' ability to kill virus-infected host cells, in spite of normal cytokine levels, and this may increase susceptibility to viral infections . This reduction in the potential ability of NK cells to kill virus-infected host cells may increase the susceptibility to viral infections after DEP exposure.
Hypomanic shift observed during rTMS treatment of patients with unipolar depressive disorder: four case reports
Authors: Ozten Eylem , Sayar Gokben Hizli , Karamustafalioglu Oguz
Published: April 2013

Objective

Repetitive transcranial magnetic stimulation (rTMS) can enhance the excitement of the brain through adjusting the biological activities of the cerebral cortex and has wide biological effects, making it one basic mechanism of therapy for depression. In the treatment of unipolar depressive disorder, almost in every treatment method, hypomanic and manic shifts can be observed. There is still a lack of data regarding manic and hypomanic symptoms triggered by rTMS applications.

Method

We describe four cases with unipolar depression in which high-frequency rTMS over the left dorsolateral prefrontal cortex applied as an add-on antidepressive strategy may have induced a hypomanic episode.

Results

In these cases, 25 Hz rTMS combined with antidepressants may have contributed to the occurrence of hypomanic symptoms.

Conclusion

Using an intensive methodology of rTMS may induce hypomanic or manic symptoms.
Genome-wide analysis reveals downregulation of miR-379/miR-656 cluster in human cancers
Authors: Laddha Saurabh V , Nayak Subhashree , Paul Deepanjan , Reddy Rajasekhara , Sharma Charu , Jha Prerana , Hariharan Manoj , Agrawal Anurag , Chowdhury Shantanu , Sarkar Chitra , Mukhopadhyay Arijit
Published: April 2013

Background

MicroRNAs (miRNAs) are non-uniformly distributed in genomes and ~30% of the miRNAs in the human genome are clustered. In this study we have focused on the imprinted miRNA cluster miR-379/miR-656 on 14q32.31 (hereafter C14) to test their coordinated function. We have analyzed expression profile of >1000 human miRNAs in >1400 samples representing seven different human tissue types obtained from cancer patients along with matched and unmatched controls.

Results

We found 68% of the miRNAs in this cluster to be significantly downregulated in glioblastoma multiforme (GBM), 61% downregulated in kidney renal clear cell carcinoma (KIRC), 46% in breast invasive carcinoma (BRCA) and 14% in ovarian serous cystadenocarcinoma (OV). On a genome-wide scale C14 miRNAs accounted for 12-30% of the total downregulated miRNAs in different cancers. Pathway enrichment for the predicted targets of C14 miRNA was significant for cancer pathways, especially Glioma (p< 3.77x10-6, FDR<0.005). The observed downregulation was confirmed in GBM patients by real-time PCR, where 79% of C14 miRNAs (34/43) showed downregulation. In GBM samples, hypermethylation at C14 locus (p<0.003) and downregulation of MEF2, a crucial transcription factor for the cluster was observed which likely contribute to the observed downregulation of the entire miRNA cluster.

Conclusion

We provide compelling evidence that the entire C14 miRNA cluster is a tumor suppressor locus involved in multiple cancers, especially in GBM, and points toward a general mechanism of coordinated function for clustered miRNAs.

Reviewers

Reviewed by: Prof. Gregory J Goodall and Dr. Alexander Max Burroughs
Metabolic engineering of Escherichia coli for high-specificity production of isoprenol and prenol as next generation of biofuels
Authors: Zheng Yanning , Liu Qiang , Li Lingling , Qin Wen , Yang Jianming , Zhang Haibo , Jiang Xinglin , Cheng Tao , Liu Wei , Xu Xin , Xian Mo
Published: April 2013

Background

The isopentenols, including isoprenol and prenol, are excellent alternative fuels. However, they are not compounds largely accumulated in natural organism. The need for the next generation of biofuels with better physical and chemical properties impels us to develop biosynthetic routes for the production of isoprenol and prenol from renewable sugar. In this study, we use the heterogenous mevalonate-dependent (MVA) isoprenoid pathway for the synthesis of isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) intermediates, and then convert IPP and DMAPP to isoprenol and prenol, respectively.

Results

A mevalonate titer of 1.7 g/L was obtained by constructing an efficient MVA upper pathway in engineered E. coli. Different phosphatases and pyrophosphatases were investigated for their abilities in hydrolyzing the IPP and DMAPP. Consequently, ADP-ribose pyrophosphatase was found to be an efficient IPP and DMAPP hydrolase. Moreover, ADP-ribose pyrophosphatase from Bacillus subtilis (BsNudF) exhibited a equivalent substrate specificity towards IPP and DMAPP, while ADP-ribose pyrophosphatase from E. coli (EcNudF) presented a high substrate preference for DMAPP. Without the expression of any phosphatases or pyrophosphatases, a background level of isopentenols was synthesized. When the endogenous pyrophosphatase genes (EcNudF and yggV) that were capable of enhancing the hydrolyzation of the IPP and DMAPP were knocked out, the background level of isopentenols was still obtained. Maybe the synthesized IPP and DMAPP were hydrolyzed by some unknown hydrolases of E. coli. Finally, 1.3 g/L single isoprenol was obtained by blocking the conversion of IPP to DMAPP and employing the BsNudF, and 0.2 g/L ~80% prenol was produced by employing the EcNudF. A maximal yield of 12% was achieved in both isoprenol and prenol producing strains.

Conclusions

To the best of our knowledge, this is the first successful report on high-specificity production of isoprenol and prenol by microbial fermentation. Over 1.3 g/L isoprenol achieved in shake-flask experiments represents a quite encouraging titer of higher alcohols. In addition, the substrate specificities of ADP-ribose pyrophosphatases were determined and successfully applied for the high-specificity synthesis of isoprenol and prenol. Altogether, this work presents a promising strategy for high-specificity production of two excellent biofuels, isoprenol and prenol.
Developmental patterns of DR6 in normal human hippocampus and in Down syndrome
Authors: Iyer Anand , van Scheppingen Jackelien , Anink Jasper , Milenkovic Ivan , Kovács Gabor G , Aronica Eleonora
Published: April 2013

Background

Death receptor 6 (DR6) is highly expressed in the human brain: it has been shown to induce axon pruning and neuron death via distinct caspases and to mediate axonal degeneration through binding to N-terminal β amyloid precursor protein (N-APP).

Methods

We investigated the expression of DR6 during prenatal and postnatal development in human hippocampus and temporal cortex by immunocytochemistry and Western blot analysis (118 normal human brain specimens; 9 to 41 gestational weeks; 1 day to 7 months postnatally; 3 to 91 years). To investigate the role of N-APP/DR6/caspase 6 pathway in the development of hippocampal Alzheimer’s disease (AD)-associated pathology, we examined DR6 immunoreactivity (IR) in the developing hippocampus from patients with Down syndrome (DS; 48 brain specimens; 14 to 41 gestational weeks; 7 days to 8 months postnatally; 15 to 64 years) and in adults with DS and AD.

Results

DR6 was highly expressed in human adult hippocampus and temporal cortex: we observed consistent similar temporal and spatial expression in both control and DS brain. Western blot analysis of total homogenates of temporal cortex and hippocampus showed developmental regulation of DR6. In the hippocampus, DR6 IR was first apparent in the stratum lacunosum-moleculare at 16 weeks of gestation, followed by stratum oriens, radiatum, pyramidale (CA1 to CA4) and molecular layer of the dentate gyrus between 21 and 23 gestational weeks, reaching a pattern similar to adult hippocampus around birth. Increased DR6 expression in dystrophic neurites was detected focally in a 15-year-old DS patient. Abnormal DR6 expression pattern, with increased expression within dystrophic neurites in and around amyloid plaques was observed in adult DS patients with widespread AD-associated neurodegeneration and was similar to the pattern observed in AD hippocampus. Double-labeling experiments demonstrated the colocalization, in dystrophic neurites, of DR6 with APP. We also observed colocalization with hyper-phosphorylated Tau and with caspase 6 (increased in hippocampus with AD pathology) in plaque-associated dystrophic neurites and within the white matter.

Conclusions

These findings demonstrate a developmental regulation of DR6 in human hippocampus and suggest an abnormal activation of the N-APP/DR6/caspase 6 pathway, which can contribute to initiation or progression of hippocampal AD-associated pathology.
Purification of crime scene DNA extracts using centrifugal filter devices
Authors: Norén Lina , Hedell Ronny , Ansell Ricky , Hedman Johannes
Published: April 2013

Background

The success of forensic DNA analysis is limited by the size, quality and purity of biological evidence found at crime scenes. Sample impurities can inhibit PCR, resulting in partial or negative DNA profiles. Various DNA purification methods are applied to remove impurities, for example, employing centrifugal filter devices. However, irrespective of method, DNA purification leads to DNA loss. Here we evaluate the filter devices Amicon Ultra 30 K and Microsep 30 K with respect to recovery rate and general performance for various types of PCR-inhibitory crime scene samples.

Methods

Recovery rates for DNA purification using Amicon Ultra 30 K and Microsep 30 K were gathered using quantitative PCR. Mock crime scene DNA extracts were analyzed using quantitative PCR and short tandem repeat (STR) profiling to test the general performance and inhibitor-removal properties of the two filter devices. Additionally, the outcome of long-term routine casework DNA analysis applying each of the devices was evaluated.

Results

Applying Microsep 30 K, 14 to 32% of the input DNA was recovered, whereas Amicon Ultra 30 K retained 62 to 70% of the DNA. The improved purity following filter purification counteracted some of this DNA loss, leading to slightly increased electropherogram peak heights for blood on denim (Amicon Ultra 30 K and Microsep 30 K) and saliva on envelope (Amicon Ultra 30 K). Comparing Amicon Ultra 30 K and Microsep 30 K for purification of DNA extracts from mock crime scene samples, the former generated significantly higher peak heights for rape case samples (P-values <0.01) and for hairs (P-values <0.036). In long-term routine use of the two filter devices, DNA extracts purified with Amicon Ultra 30 K were considerably less PCR-inhibitory in Quantifiler Human qPCR analysis compared to Microsep 30 K.

Conclusions

Amicon Ultra 30 K performed better than Microsep 30 K due to higher DNA recovery and more efficient removal of PCR-inhibitory substances. The different performances of the filter devices are likely caused by the quality of the filters and plastic wares, for example, their DNA binding properties. DNA purification using centrifugal filter devices can be necessary for successful DNA profiling of impure crime scene samples and for consistency between different PCR-based analysis systems, such as quantification and STR analysis. In order to maximize the possibility to obtain complete STR DNA profiles and to create an efficient workflow, the level of DNA purification applied should be correlated to the inhibitor-tolerance of the STR analysis system used.
The effects of hydration on the collagen and gelatine phases within parchment artefacts
Authors: Gonzalez Lee Grant , Wess Timothy James
Published: April 2013

This review discusses the need to understand the effects of relative humidity on parchment and the current understanding of parchment structure and hydration. It also provides a critical evaluation of the body of foregoing research investigating the effects of relative humidity on parchment artefacts. The critical evaluation shows that the current scientific evidence that can be used to inform the debate with regard to relative humidity guidelines for the preservation of parchment artefacts is insufficient, especially in the light of a greater understanding of parchment based documents when considered as composite materials comprising collagen and gelatine. The differential behaviour of collagen and gelatine (and consequently the effect on the interfaces between them) in terms of response to relative humidity changes, is proposed as a key factor to be considered for future studies. This review concludes with an analysis of the next steps required in parchment research in order to provide an informed advisory framework.
Alteration of pulmonary function in diabetic nephropathy
Authors: Shafiee Gita , Khamseh Mohammad E , Rezaei Nader , Aghili Rokhsareh , Malek Mojtaba
Published: April 2013

Background

Type 2 diabetes mellitus is increasing worldwide with an alarming rate. It is associated with the development of various chronic complications. The aim of this study was to explore the alteration of pulmonary function, and its association with renal complications in people with type 2 diabetes mellitus.

Methods

This cross-sectional study was conducted on three groups; 40 diabetic subjects without nephropathy (urinary albumin<30 mg/day), 40 subjects with nephropathy (urinary albumin≥30 mg/day), and 40 healthy subjects as the control group. The subjects with nephropathy were divided into those with microalbuminuria (urinary albumin=30-300 mg/day) and those with macroalbuminuria (urinary albumin>300 mg/day) .Diabetic subjects were matched to the control group in terms of age, sex, and BMI. Pulmonary function tests were performed and the results were compared between groups.

Results

Forced vital capacity (FVC; % predicted), forced expiratory volume in 1 second (FEV1; % predicted), and peak expiratory flow (PEF; % predicted) were significantly lower in subjects with diabetic nephropathy compared to the healthy controls (P<0.05). Meanwhile, in diabetic subjects, FVC and FEV1 were lower in those with diabetic nephropathy compared to those with normal albumin excretion (P<0.05). On the other hand, FEV1/FVC was significantly higher in diabetic people with nephropathy.

Furthermore, a significant difference was observed between FVC and FEV1 in diabetic people with microalbuminuria compared to those with macroalbuminuria.

Conclusions

This study showed that the pulmonary function was impaired in people with Diabetes. The progression of diabetic nephropathy to more advanced stages was also associated with more impairment of pulmonary function.
Variation in the Traditional Vowels of the Eastern States
Authors: Kretzschmar William A.
Published: April 2013

In contrast to Hans Kurath and Raven McDavid's traditional analysis of vowel variation presented in their 1961 Pronunciation of English in the Atlantic States, which was a largely intuitive, qualitative treatment of the evidence that focused on patterns of regional contrast, this study focuses on the picture of quantitative variation in American English vowels along the North Midland and South Midland border as represented in data from the Linguistic Atlas of Middle and South Atlantic States. For each of the 12 vowels studied, its various pronunciations within a single word (e.g., /i/ in three, /I/ in six, etc.) were tallied for the overall sample of 1,162 speakers and for nine subsamples, representative of three domains from the altas data: sex, education/social adjustment (three types), and occupation (four types). The results show that for each vowel, at each level of analysis, the pronunciation type/frequency rankings form a nonlinear distribution, represented graphically by an asymptotic hyperbolic curve (or A-curve), with only a few of the most frequent vowel realizations accounting for the vast majority of tokens. While there is a large amount of pronunciation overlap between regional or social groups, comparison of the type/frequency rankings shows that different groups of speakers each have different orders of the frequent variant realizations of the vowels, which helps explain how one can distinguish one group's speech from another's but does not support the traditional notion of contrast as absolute, binary, and categorical.
The a-Curve and Personally Patterned Variation: More Tools for Investigating Language Variation and Change
Authors: Sabino Robin
Published: April 2013

This article explores two variables that largely have been ignored in studies of language variation and language change: frequency and individual speaker. In doing so, it demonstrates the usefulness of the A-curve, an asymptotic hyperbolic graphic representation of language variation based on usage. Data are drawn from varieties of English: two Afro-Caribbean vernaculars (Antiguan and Negerhollands) and East Sutherland Gaelic. Because both Negerhollands and East Sutherland Gaelic were moribund when the data discussed here were collected and both are characterized by personally patterned variation, the histories of these varieties are briefly considered. The article concludes that both frequency and individual speaker are essential for a full understanding of the ways in which language users deploy their linguistic resources and, thus, are critical for our understanding of human language.
Heterogeneity in sexual bipotentiality and plasticity of granulosa cells in developing mouse ovaries
Authors: Harikae Kyoko , Miura Kento , Shinomura Mai , Matoba Shogo , Hiramatsu Ryuji , Tsunekawa Naoki , Kanai-Azuma Masami , Kurohmaru Masamichi , Morohashi Ken-ichirou , Kanai Yoshiakira
Published: April 2013

In mammalian sex determination, SRY directly upregulates the expression of SOX9, the master regulatory transcription factor in Sertoli cell differentiation, leading to testis formation. Without SRY action, the bipotential gonadal cells become pre-granulosa cells, which results in ovarian follicle development. When, where and how pre-granulosa cells are determined to differentiate into developing ovaries, however, remains unclear. By monitoring SRY-dependent SOX9-inducibility (SDSI) in a Sry-inducible mouse system, here we show spatiotemporal changes in the sexual bipotentiality/plasticity of ovarian somatic cells throughout a life. The early pre-granulosa cells maintain the SDSI until 11.5 dpc, after which most pre-granulosa cells rapidly lose this ability by 12.0 dpc. Unexpectedly, we found a subpopulation of the pre-granulosa cells near the mesonephric tissue that continuously retains SDSI throughout fetal and early postnatal stages. After birth, these SDSI-positive pre-granulosa cells contribute to the initial round of folliculogenesis by secondary follicle stage. In experimental sex reversal of 13.5-dpc ovaries grafted into adult male nude mice, the differentiated granulosa cells reacquire the SDSI before other signs of masculinization. Our data provide direct evidence of an unexpectedly high sexual heterogeneity of granulosa cells in developing mouse ovaries in a stage- and region-specific manner. Discovery of such sexually bipotential granulosa cells provides a novel entry point to the understanding of masculinization in various cases of XX disorders of sexual development in mammalian ovaries.
Spatiotemporal organization of Aurora-B by APC/CCdh1 after mitosis coordinates cell spreading via FHOD1
Authors: Floyd Suzanne , Whiffin Nicola , Gavilan Maria P. , Kutscheidt Stefan , De Luca Maria , Marcozzi Chiara , Min Mingwei , Watkins Johnathan , Chung Kathryn , Fackler Oliver T. , Lindon Catherine
Published: April 2013

Spatiotemporal regulation of mitotic kinase activity underlies the extensive rearrangement of cellular components required for cell division. One highly dynamic mitotic kinase is Aurora kinase B (AurB), which has multiple roles defined by the changing localization of the chromosome passenger complex (CPC) as cells progress through mitosis, including regulation of cytokinesis and abscission. Like other mitotic kinases, AurB is a target of the anaphase-promoting complex (APC/C) ubiquitin ligase during mitotic exit, but it is not known if APC/C-mediated destruction plays any specific role in controling AurB activity. Here we have examined the contribution of APC/CCdh1 to organization of AurB activity as cells exit mitosis and re-enter interphase. We report that APC/CCdh1-dependent proteolysis restricts a cell cortex-associated pool of active AurB in space and time. In early G1 phase this pool of AurB is found at protrusions associated with cell spreading. AurB retention at the cortex depends on a formin, FHOD1, critically required to organize the cytoskeleton after division. We identify AurB phosphorylation sites in FHOD1 and show that phosphomutant FHOD1 is impaired in post-mitotic assembly of oriented actin cables. We propose that Cdh1 contributes to spatiotemporal organization of AurB activity and that organization of FHOD1 activity by AurB contributes to daughter cell spreading after mitosis.
Wnt/β-catenin pathway represses let-7 microRNAs expression via transactivation of Lin28 to augment breast cancer stem cell expansion
Authors: Cai Wang-Yu , Wei Tong-Zhen , Luo Qi-Cong , Wu Qiu-Wan , Liu Qing-Feng , Yang Meng , Ye Guo-Dong , Wu Jia-Fa , Chen Yuan-Yuan , Sun Guang-Bin , Liu Yun-Jia , Zhao Wen-Xiu , Zhang Zhi-Ming , Li Bo-An
Published: April 2013

Wnt signaling through β-catenin and the lymphoid-enhancing factor 1/T-cell factor (LEF1/TCF) family of transcription factors maintains stem cell properties in both normal and malignant tissues; however, the underlying molecular pathway involved in this process has not been completely defined. Using a microRNA microarray screening assay, we identified the let-7 miRNAs as downstream targets of Wnt/β-catenin pathway. Expression studies indicated that Wnt/β-catenin pathway suppresses mature let-7 miRNAs but not the primary transcripts, which suggests a posttranscriptional regulation of repression. Furthermore, we identified Lin28, a negative let-7 biogenesis regulator, as a novel direct downstream target of Wnt/β-catenin pathway. Loss of function of Lin28 impairs the Wnt/β-catenin pathway-mediated let-7 inhibition and breast cancer stem cell expansion; enforced expression of let-7 blocks the Wnt/β-catenin pathway-stimulated breast cancer stem cell phenotype. Finally, we demonstrated that Wnt/β-catenin pathway induces Lin28 upregulation and let-7 downregulation in both cancer samples and mouse tumour models. Moreover, the delivery of a modified lin28 siRNA or a let-7a agomir into the premalignant mammary tissues of MMTV-wnt-1 mice resulted in a complete rescue of the stem cell phenotype driven by Wnt/β-catenin pathway. These findings highlight a pivotal role for Lin28/let-7 in Wnt/β-catenin pathway mediated cellular phenotypes. Thus, Wnt/β-catenin pathway, Lin28, and let-7 miRNAs, three of the most crucial stem cell regulators, connect in one signal cascade.
The complement membrane attack complex triggers intracellular Ca2+ fluxes leading to NLRP3 inflammasome activation
Authors: Triantafilou Kathy , Hughes Timothy R. , Triantafilou Martha , Morgan B. Paul
Published: April 2013

The membrane attack complex of complement (MAC), apart from its classical role of lysing cells, can also trigger a range of non-lethal effects on cells, acting as a drive to inflammation. In this study we chose to investigate these non-lethal effects on inflammasome activation. We found that, following sublytic MAC attack, there is increased cytosolic Ca2+ concentration, at least partly through Ca2+ release from the endoplasmic reticulum lumen via the inositol 1,4,5-triphosphate receptor (IP3R) and ryanodine receptor (RyR) channels. This increase in intracellular Ca2+ concentration leads to Ca2+ accumulation into the mitochondrial matrix via MICU1, the “mitochondrial calcium uniporter” (MCU), loss of mitochondrial transmembrane potential, triggering NLRP3 inflammasome activation and IL-1β release. NLRP3 co-localises with the mitochondria, likely sensing the increase in calcium and the resultant mitochondrial dysfunction, leading to caspase activation and apoptosis. This is the first study that links non-lethal effects of sublytic MAC attack with inflammasome activation and provides a mechanism by which sublytic MAC can drive inflammation and apoptosis.
Apicobasal secretion of Wnt11 and Wnt3a in polarized epithelial cells is regulated by distinct mechanisms
Authors: Yamamoto Hideki , Awada Chihiro , Hanaki Hideaki , Sakane Hiroshi , Tsujimoto Ikuko , Takahashi Yuko , Takao Toshifumi , Kikuchi Akira
Published: April 2013

Wnts are glycan- and lipid-modified morphogens that are important for cellular responses, but how Wnt is secreted in polarized epithelial cells remains unclear. Although Wntless (Wls) has been shown to interact with Wnts and support their secretion, the role of Wls in the sorting of Wnts to the final destination in polarized epithelial cells have not been clarified. Glycosylation was shown to be important for the sorting of some transmembrane and secreted proteins, but glycan profiles and their roles in the polarized secretion of Wnts are not known. Here we show the apicobasal secretion of Wnts is regulated by different mechanisms. Wnt11 and Wnt3a were secreted apically and basolaterally, respectively, in polarized epithelial cells. Wls was localized to the basolateral membrane. Mass-spectrometric analyses revealed that Wnt11 is modified with complex/hybrid-(Asn40), high-mannose-(Asn90), and high-mannose/hybrid-(Asn300) type glycans and that Wnt3a is modified with two high-mannose-type glycans (Asn87 and Asn298). Glycosylation processing at Asn40 and galectin-3 were required for the apical secretion of Wnt11, while clathrin and adaptor protein-1 were required for the basolateral secretion of Wnt3a. By the fusion of the Asn40 glycosylation site of Wnt11, Wnt3a was secreted apically. The recycling of Wls by AP-2 was necessary for the basolateral secretion of Wnt3a but not for the apical secretion of Wnt11. These results suggest that Wls has different roles on the polarized secretion of Wnt11 and Wnt3a and that glycosylation processing of Wnts decides their secretory routes.
Nuclear proteins that become part of the mitotic apparatus: A role in nuclear assembly?
Authors: Pettijohn D. E. , Henzl M. , Price C.
Published: April 2013

A structure located at the poles of the mitotic spindle is described, which may function as a centre for post-mitotic nuclear assembly. Evidence in support of this function is incomplete, but comes from two different kinds of experiments, which are reviewed here. First, fluorescence microscopy studies show that mitotic chromosomes at telophase or late anaphase are drawn into juxtaposition with this polar structure and second, the structure is made up in part of a non-histone chromosomal protein that in interphase cells can be detected only in the nucleus. Studies of this nuclear-mitotic apparatus protein (NuMA protein) are reported here. Monoclonal antibodies specific for the NuMA protein have been used in immunofluorescence studies to visualize the prenucleus-like polar structure and to identify the NuMA protein by immunoblotting after electrophoretic separation. The NuMA protein is a non-histone chromosomal protein of molecular weight 250 000 relative to standard protein molecular weight markers in sodium dodecyl sulphate/polyacrylamide gel electrophoresis. Experiments are described that indicate several difficulties in studying the possible affinity and association of NuMA protein with mitotic chromosomes. Metaphase chromosomes isolated by the polyamine procedure of Lewis and Laemmli have bound NuMA protein detectable by immunofluorescence or by immunoblotting, but measurements made at different stages of chromosome purification show that most of the NuMA protein is separated from the chromosomes using this purification procedure. Chromosomes purified from mixtures of human and Chinese hamster cells (the latter have none of the human form of NuMA recognized by a monoclonal antibody) have human NuMA protein bound to the hamster chromosomes. Results suggest that in cell extracts exchange reactions of NuMA protein can occur, which must be avoided in the study of its natural function.
The ultrastructural organization of prematurely condensed chromosomes
Authors: Gollin Susanne M. , Wray Wayne , Hanks Steven K. , Hittelman Walter N. , Rao Potu N.
Published: April 2013

In an effort to understand the arrangement of the basic 30 nm chromatin fibre within metaphase chromosomes, changes in the organization of prematurely condensed chromosomes (PCC) were examined as a function of progression through the cell cycle. The structural features of PCC observed under the light microscope were compared with those obtained by scanning electron microscopy. PCC with varying levels of condensation were obtained by fusing mitotic HeLa cells with interphase cells synchronized at different times in the cell cycle. PCC from G1 cells are composed of rather tightly packed bundles of tortuous chromatin fibres. The density of fibre packing along the longitudinal axis of G1-phase PCC is lower and less uniform than that of metaphase chromosomes. Early G1 PCC exhibit gyres suggesting a despiralized chromonema. The condensed domains in G1 PCC appear to be organized as supercoiled loops; whereas fibre-sparse domains consist of longitudinal fibres running along the chromosome axis. As cells progressed towards S phase, a greater proportion of highly extended regions containing prominent longitudinal fibres became evident in the PCC. The pulverized appearance of S-phase PCC under the light microscope corresponded to the highly condensed, looping fibre domains separated by more extended segments containing longitudinal fibres that are visualized using the scanning electron microscope. Active sites of DNA synthesis are implicated to be localized within extended longitudinal fibres. Post-replicative chromosome maturation extends through the G2 period and appears to involve rearrangement of the extended longitudinal fibres into packed looping-fibre clusters, which then coalesce.

These observations support the model for packing DNA into chromosomes proposed in 1980 by Mullinger & Johnson. Briefly, this model suggests that the chromonema of each metaphase chromatid contains regions composed of folded longitudinal chromatin fibres as well as looping fibres that emerge from the axis at distinct foci. The final level of chromatin packing in metaphase chromosomes is attained by spiralization of the chromonema.
DNA supercoiling and its effects on the structure of DNA
Authors: Wang James C.
Published: April 2013

In prokaryotic organisms, there is strong evidence that the DNA is underwound or negatively supercoiled. The degree of supercoiling of intracellular DNA is less certain, and various estimates that can be made from existing data place the specific linking difference (superhelical density) of intracellular DNA in prokaryotes around –0·04. The effects of negative supercoiling on DNA structure are illustrated by the flipping of alternating C-G or T-G sequences from right-handed B- helical form to the left-handed Z-helical form. For a plasmid containing a 42 base-pair alternating C-G insert, the B-to-Z transition occurs at a specific linking difference of –0·031 in a dilute aqueous buffer; the same transition occurs at a specific linking difference of —0·041 for a plasmid containing a 42 base-pair alternating T-G insert. The probing of the structure of a particular sequence of intracellular DNA is discussed.