bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of Variance Components Reveals the Contribution of Sample Processing to Transcript Variation
Authors: van der Veen Douwe , Oliveira José Miguel , van den Berg Willy A. M. , de Graaff Leo H.
Published: February 2009

The proper design of DNA microarray experiments requires knowledge of biological and technical variation of the studied biological model. For the filamentous fungusAspergillus niger, a fast, quantitative real-time PCR (qPCR)-based hierarchical experimental design was used to determine this variation. Analysis of variance components determined the contribution of each processing step to total variation: 68% is due to differences in day-to-day handling and processing, while the fermentor vessel, cDNA synthesis, and qPCR measurement each contributed equally to the remainder of variation. The global transcriptional response tod-xylose was analyzed using Affymetrix microarrays. Twenty-four statistically differentially expressed genes were identified. These encode enzymes required to degrade and metabolized-xylose-containing polysaccharides, as well as complementary enzymes required to metabolize complex polymers likely present in the vicinity ofd-xylose-containing substrates. These results confirm previous findings that thed-xylose signal is interpreted by the fungus as the availability of a multitude of complex polysaccharides. Measurement of a limited number of transcripts in a defined experimental setup followed by analysis of variance components is a fast and reliable method to determine biological and technical variation present in qPCR and microarray studies. This approach provides important parameters for the experimental design of batch-grown filamentous cultures and facilitates the evaluation and interpretation of microarray data.
Culture-Independent Characterization of Bacterial Communities Associated with the Cold-Water Coral
Lophelia pertusa
in the Northeastern Gulf of Mexico
Authors: Kellogg Christina A. , Lisle John T. , Galkiewicz Julia P.
Published: February 2009

Bacteria are recognized as an important part of the total biology of shallow-water corals. Studies of shallow-water corals suggest that associated bacteria may benefit the corals by cycling carbon, fixing nitrogen, chelating iron, and producing antibiotics that protect the coral from other microbes. Cold-water or deep-sea corals have a fundamentally different ecology due to their adaptation to cold, dark, high-pressure environments and as such have novel microbiota. The goal of this study was to characterize the microbial associates of
Lophelia pertusa
in the northeastern Gulf of Mexico. This is the first study to collect the coral samples in individual insulated containers and to preserve coral samples at depth in an effort to minimize thermal shock and evaluate the effects of environmental gradients on the microbial diversity of samples. Molecular analysis of bacterial diversity showed a marked difference between the two study sites, Viosca Knoll 906/862 (VK906/862) and Viosca Knoll 826 (VK826). The bacterial communities from VK826 were dominated by a variety of unknown mycoplasmal members of the
Tenericutes
and
Bacteroidetes
, whereas the libraries from VK906/862 were dominated by members of the
Proteobacteria
. In addition to novel sequences, the 16S rRNA gene clone libraries revealed many bacterial sequences in common between Gulf of Mexico
Lophelia
corals and Norwegian fjord
Lophelia
corals, as well as shallow-water corals. Two
Lophelia
-specific bacterial groups were identified: a cluster of gammaproteobacteria related to sulfide-oxidizing gill symbionts of seep clams and a group of
Mycoplasma
spp. The presence of these groups in both Gulf and Norwegian
Lophelia
corals indicates that in spite of the geographic heterogeneity observed in
Lophelia
-associated bacterial communities, there are
Lophelia
-specific microbes.
Structural Insights into the Extracytoplasmic Thiamine-Binding Lipoprotein p37 of
Mycoplasma hyorhinis
Authors: Sippel Katherine H. , Robbins Arthur H. , Reutzel Robbie , Boehlein Susan K. , Namiki Kazunori , Goodison Steve , Agbandje-McKenna Mavis , Rosser Charles J. , McKenna Robert
Published: February 2009

The
Mycoplasma hyorhinis
protein p37 has been implicated in tumorigenic transformation for more than 20 years. Though there are many speculations as to its function, based solely on sequence homology, the issue has remained unresolved. Presented here is the 1.6-Å-resolution refined crystal structure of
M. hyorhinis
p37, renamed the extracytoplasmic thiamine-binding lipoprotein (Cypl). The structure shows thiamine pyrophosphate (TPP) and two calcium ions are bound to Cypl and give the first insights into possible functions of the Cypl-like family of proteins. Sequence alignments of Cypl-like proteins between several different species of mycoplasma show that the thiamine-binding site is likely conserved and structural alignments reveal the similarity of Cypl to various binding proteins. While the experimentally determined function of Cypl remains unknown, the structure shows that the protein is a TPP-binding protein, opening up many avenues for future mechanistic studies and making Cypl a possible target for combating mycoplasma infections and tumorigenic transformation.
Health consequences of sustained smoking cessation
Authors: Bjartveit K , Tverdal A
Published: February 2009

Objectives:

To estimate the risk of dying from all causes and from specified smoking-related diseases in people who were ex-smokers at two consecutive examinations, compared with never smokers and with people who were ex-smokers at the first examination but who had resumed smoking at the following examination.

Design:

A prospective cohort study.

Setting:

Three counties in Norway.

Participants:

A total of 23 560 men and 25 122 women, aged 20–49, screened for cardiovascular disease risk factors in the mid 1970s, rescreened after 3–13 years and followed throughout 2005 participated in this study.

Outcomes:

Absolute mortality and relative risks adjusted for confounding variables, of dying from all causes, cardiovascular disease, ischaemic heart disease, stroke, lung cancer and other smoking-related cancer.

Results:

With sustained never smokers as reference, the sustained ex-smokers had adjusted relative risk (95% CI), of dying from any cause, for men 0.97 (0.80 to 1.18), for women 0.98 (0.65 to 1.48). Corresponding risk for ex-smokers who resumed smoking was for men 1.59 (1.32 to 1.91), for women 1.40 (1.08 to 1.81). For the specified smoking-related diseases, the risk in sustained ex-smokers was not significantly different from the risk in sustained never-smokers, except for lung cancer in men. For ex-smokers who resumed smoking, the corresponding risk was on the whole significantly higher.

Conclusions:

A more valid and favourable picture of ex-smokers’ risk will be obtained if exposure is being based upon people with two consecutive examinations, years apart. The study confirms clearly the large health benefit of quitting smoking for good.
Characterization of new polymorphic functional markers for sugarcane
Authors: Oliveira K. M. , Pinto L. R. , Marconi T. G. , Mollinari M. , Ulian E. C. , Chabregas S. M. , Falco M. C. , Burnquist W. , Garcia A. A.F. , Souza A. P.
Published: February 2009

Expressed sequence tags (ESTs) offer the opportunity to exploit single, low-copy, conserved sequence motifs for the development of simple sequence repeats (SSRs). The authors have examined the Sugarcane Expressed Sequence Tag database for the presence of SSRs. To test the utility of EST-derived SSR markers, a total of 342 EST–SSRs, which represent a subset of over 2005 SSR-containing sequences that were located in the sugarcane EST database, could be designed from the nonredundant SSR-positive ESTs for possible use as potential genic markers. These EST–SSR markers were used to screen 18 sugarcane ( Saccharum spp.) varieties. A high proportion (65.5%) of the above EST–SSRs, which gave amplified fragments of foreseen size, detected polymorphism. The number of alleles ranged from 2 to 24 with an average of 7.55 alleles per locus, while polymorphism information content values ranged from 0.16 to 0.94, with an average of 0.73. The ability of each set of EST–SSR markers to discriminate between varieties was generally higher than the polymorphism information content analysis. When tested for functionality, 82.1% of these 224 EST–SSRs were found to be functional, showing homology to known genes. As the EST–SSRs are within the expressed portion of the genome, they are likely to be associated to a particular gene of interest, improving their utility for genetic mapping; identification of quantitative trait loci, and comparative genomics studies of sugarcane. The development of new EST–SSR markers will have important implications for the genetic analysis and exploitation of the genetic resources of sugarcane and related species and will provide a more direct estimate of functional diversity.
Genetic diversity analysis in blackgram (Vigna mungo (L.) Hepper) using AFLP and transferable microsatellite markers from azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi)
Authors: Gupta S. K. , Gopalakrishna T.
Published: February 2009

Genetic diversity in 20 elite blackgram ( Vigna mungo (L.) Hepper) genotypes was studied using microsatellite and AFLP markers. Thirty-six microsatellite markers from azuki bean ( Vigna angularis (Willd.) Ohwi & Ohashi) were successfully amplified across the 20 blackgram genotypes and 33 microsatellite markers showed polymorphism. A total of 137 microsatellite alleles were generated with an average of 4.1 alleles per locus. The number of alleles ranged from two to nine and the polymorphic information content value for the microsatellite markers varied from 0.10 to 0.87 with an average of 0.49. Microsatellite markers were highly informative and a combination of only three microsatellite markers (CEDG264, CEDG173, and CEDG044) was sufficient to discriminate all 20 blackgram genotypes. In the case of AFLP, 11 primer pairs generated 324 polymorphic marker fragments. The polymorphic information content values for AFLP primer combinations ranged from 0.21 to 0.34 with an average of 0.29. Similarity measures and clustering analyses were made using microsatellite and AFLP data separately. The resulting dendrograms distributed the 20 blackgram genotypes into five main clusters. The dendrograms were comparable with each other with the Mantel test between the cophenetic matrices of microsatellite data and AFLP data showing moderate correlation (r = 0.64). The results of the principal components analysis were well congruent with the dendrograms. In the dendrograms as well as in the principal components analyses, genotype Trombay wild (Vigna mungo var. silvestris) was placed separately from rest of the genotypes. This study demonstrated that the azuki bean microsatellite markers are highly polymorphic and informative and can be successfully used for genome analysis in blackgram. Results indicate that sufficient variability is present in the blackgram genotypes and would be helpful in the selection of suitable parents for breeding purposes and gene mapping studies.
The heat shock 70 genes of the olive pest Bactrocera oleae: genomic organization and molecular characterization of a transcription unit and its proximal promoter region
Authors: Drosopoulou Elena , Chrysopoulou Anastasia , Nikita Venetia , Mavragani-Tsipidou Penelope
Published: February 2009

A Bactrocera oleae genomic library was constructed and several genomic clones bearing hsp70 sequences were isolated. All clones were in situ hybridized on the major heat shock puff locus of the salivary gland polytene chromosomes. Restriction mapping of the isolated clones and genomic Southern hybridization indicated the presence of several putative hsp70 genes organized in a single cluster. Sequence analysis of an hsp70 transcription unit revealed a single 1905 nt long open reading frame that exhibits characteristic features of the inducible members of the HSP70 family. The presence and organization of many typical binding sites for the Heat Shock and GAGA factors suggest that the promoter of this gene is highly heat-inducible and could be used for conditional expression in transformation systems.
HcrVfparalogs are present on linkage groups 1 and 6 ofMalus
Authors: Broggini Giovanni A.L. , Galli Paolo , Parravicini Gabriella , Gianfranceschi Luca , Gessler Cesare , Patocchi Andrea
Published: February 2009

Molecular markers derived from resistance gene analogs of HcrVf2, the first apple resistance gene cloned, may pave the way to the cloning of additional apple scab resistance genes. The Malus ×domestica ‘Florina’ (Vf) bacterial artificial chromosome (BAC) genomic library was screened by hybridization using HcrVf2 as a probe. Positive BAC clones were assembled into contigs and microsatellite markers developed from each contig mapped. Only linkage groups 1 and 6 contained HcrVf2 paralogs. On linkage group 1, five loci in addition to the Vf locus were identified. A single locus was detected on linkage group 6. Representative BAC clones of these loci including the Vf locus were sequenced and the gene structure compiled. A total of 22 sequences, showing high sequence similarity to HcrVf2, were identified. Nine sequences were predicted to encode all seven protein domains described in HcrVf2, while three were truncated. Transcriptional analysis indicated that six genes with a complete HcrVf-like structure were constitutively expressed in young uninfected leaves of ‘Florina’. The map position of each HcrVf analog was compared with the location of the major apple scab resistance genes. None of the major genes conferring scab resistance co-localized with HcrVf paralogs, indicating that they are unlikely to belong to the leucine-rich repeat – transmembrane class, which includes the Vf gene.
The correlations of the function and positional distribution of the cis-elements CArG around the TSS in the genes of Mus musculus
Authors: Shen Xia , Walsh Bruce , Li Jing J. , Pang Hong X. , Wang Wen J. , Tao Shi H.
Published: February 2009

While many studies of cis-elements CArG bound by serum response factor (SRF) are in progress, little is known about the positional distribution of the functional CArG elements around the transcription start site (TSS) of genes that they influence. We use a validated CArG data set to calculate the distance distribution of functional CArG elements around the TSS. Distances between adjacent CArGs were also analyzed. We compare these distributions with those derived using a control set of randomly selected CArGs (that were not experimentally validated for function). Our results show that most functional CArG elements (108 of 152, 71%) exist upstream of the annotated TSS, with copy number increasing as one moves closer to the TSS. Moreover, the average number of the CArG elements in the CArG-containing genes is significantly more than that in the control genes. Our study extends earlier bioinformatic analyses of functional CArG elements and provides an application of comparative sequence data to the identification of transcription factor binding sites.
Genetic analysis and historical perspective of cashew (Anacardium occidentaleL.) introduction into India
Authors: Archak S. , Gaikwad A. B. , Swamy K. R.M. , Karihaloo J. L.
Published: February 2009

Cashew ( Anacardium occidentale L.), introduced into India about 400 years ago, is distributed widely in the coastal regions as spontaneous populations as well as in cultivation. Despite the plant’s commercial exploitation, little is known about its actual introduction and diversification. We attempted to construct these events by investigating the level of genetic variation and genetic structure of cashew populations collected from different geographical regions of India. A total of 91 individuals from four populations were analysed using AFLP markers and morphometric data. AFLP analysis based on 354 polymorphic loci revealed Indian cashew to have low but relatively substantial genetic diversity for an introduced species (HE = 0.262 and IS = 0.404). Twenty-seven qualitative and quantitative traits also revealed the existence of considerable morphometric variation (24% around the mean values). Bayesian cluster analysis based on AFLP data did not indicate the existence of definite population differentiation. Morphometric analysis allocated 12% variation among all four populations, whereas AFLP variation observed in cashew individuals was entirely within populations. The results, supporting the possibility of cashew having been introduced into India repeatedly over a period of time but at a single location (west coast), are discussed and their implications for germplasm management are described.
The roles of IL-6 in the regulation of glucose homeostasis
Authors: Gusba Jenny E.
Published: February 2009

This thesis examined the roles of interleukin (IL)-6 in the regulation of glucose homeostasis, with a specific focus on skeletal muscle. Study 1 sought to determine whether muscle glycogen content is a stimulus for the production of IL-6, examining the periods during and after exercise. The relationship between IL-6 and muscle glycogen content was measured during similar bouts of exhaustive exercise on 2 occasions that resulted in large increases in muscle messenger (m)RNA for IL-6 and circulating levels of IL-6. On 1 occasion, subjects received carbohydrate during recovery to facilitate rates of glycogen resynthesis. During exercise, subjects performed similar bouts of exercise, such that differences in an individual’s glycogen levels between trials could be compared with differences in IL-6. No correlation was detected between the net change in glycogen content and the net change in plasma IL-6 or IL-6 mRNA from rest to exhaustion. Moreover, when the difference within subjects at exhaustion in IL-6 and glycogen was compared, there was no correlation between the 2 variables. During recovery, although carbohydrate intake significantly increased glycogen resynthesis, there was no change in postexercise IL-6 mRNA level or plasma IL-6 concentration. Therefore, glycogen was not the sole regulator of IL-6 production in skeletal muscle. Study 2 examined the direct effect of IL-6 and tumor necrosis factor (TNF)-α on glucose transport and the phosphorylation of key signalling proteins with or without insulin and during rodent muscle contraction. Under basal conditions, IL-6 increased glucose transport in association with an increase in 5′AMP-activated protein kinase (AMPK) and AS160 phosphorylation, but IL-6 decreased insulin-stimulated glucose transport via a reduction in phosphorylation of calcium–calmodulin-dependent protein kinase (CaMK)II and AS160. A novel finding generated from these experiments was the direct involvement of IL-6 in contraction-mediated glucose transport. In the case of muscle contraction, IL-6 was found to increase the phosphorylation of CaMKII and AS160. This research suggests that the activation of CaMKII is involved in the actions of IL-6 under insulin-stimulated and contraction-mediated conditions. Furthermore, AS160 was identified as a common signalling intermediate, influenced by IL-6. It also suggests that AS160 may be a point of convergence for multiple signalling pathways. Finally, the actions of TNF-α mimicked those of IL-6, except during contraction, where TNF-α had no significant effect on glucose transport and attenuated the effects of IL-6.
Physical activity, cardiorespiratory fitness, and metabolic syndrome in young Mexican and Mexican-American women
Authors: Vella Chantal A. , Zubia Raul Y. , Ontiveros Diana , Cruz Martha L.
Published: February 2009

Young adult women have had the greatest increase in prevalence of metabolic syndrome (MetS) over time, and prevalence is highest in Hispanic women, compared with women of other ethnicities. Factors contributing to the high prevalence of MetS in Hispanic women are unknown. This study was conducted to determine if physical activity or fitness were associated with individual features of MetS in young Mexican and Mexican-American women, and if the associations were independent of fat mass. Sixty young Mexican and Mexican-American women participated in the study. MetS was defined according to the Adult Treatment Panel III. A fasting blood sample was drawn for the measurement of glucose, insulin, high-density lipoprotein cholesterol (HDL-c), and triglycerides. Physical activity was assessed by questionnaire and accelerometer. Fitness was assessed by progressive treadmill test to exhaustion and ventilatory threshold. Body composition was assessed with Bod Pod. Multivariate regression was used to establish the independent contributions of physical activity and fitness to the individual features of MetS. After controlling for fat mass and fat-free mass, physical activity was found to be independently related to HDL-c and fitness was found to be independently related to triglycerides (p < 0.05). The independent associations between physical activity, fitness, and features of MetS were mediated by, rather than independent of, fat mass. Fat mass was independently related to triglycerides, systolic blood pressure, and diastolic blood pressure. Although physical activity and fitness were related to features of MetS, these associations were not independent of fat mass.
Transcription-factor-mediated epigenetic control of cell fate and lineage commitmentThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.
Authors: Stein Gary S. , Zaidi Sayyed K. , Stein Janet L. , Lian Jane B. , van Wijnen Andre J. , Montecino Martin , Young Daniel W. , Javed Amjad , Pratap Jitesh , Choi Je-Yong , Ali Syed A. , Pande Sandhya , Hassan Mohammad Q.
Published: February 2009

Epigenetic control is required to maintain competency for the activation and suppression of genes during cell division. The association between regulatory proteins and target gene loci during mitosis is a parameter of the epigenetic control that sustains the transcriptional regulatory machinery that perpetuates gene-expression signatures in progeny cells. The mitotic retention of phenotypic regulatory factors with cell cycle, cell fate, and tissue-specific genes supports the coordinated control that governs the proliferation and differentiation of cell fate and lineage commitment.
Untargeted tail acetylation of histones in chromatin: lessons from yeastThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.
Authors: Friis R. Magnus N. , Schultz Michael C.
Published: February 2009

Dynamic acetylation of lysine residues in the amino-terminal tails of the core histones is functionally important for the regulation of diverse DNA-dependent processes in the nucleus, including replication, transcription, and DNA repair. The targeted and untargeted activities of histone lysine acetylases (KATs) and deacetylases (HDACs) both contribute to the dynamics of chromatin acetylation. While the mechanisms and functional consequences of targeted on histone acetylation are well understood, relatively little is known about untargeted histone acetylation. Here, we review the current understanding of the mechanisms by which untargeted KAT and HDAC activities modulate the acetylation state of nucleosomal histones, focusing on results obtained for H3 and H4 in budding yeast. We also highlight unresolved problems in this area, including the question of how a particular steady-state level of untargeted acetylation is set in the absence of cis-dependent mechanisms that instruct the activity of KATs and HDACs.
The molecular basis of chromatin dynamics during nucleotide excision repairThis paper is one of a selection of papers published in this Special Issue, entitled 29th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.
Authors: Zhang Ling , Jones Kristi , Gong Feng
Published: February 2009

The assembly of DNA into chromatin in eukaryotic cells affects all DNA-related cellular activities, such as replication, transcription, recombination, and repair. Rearrangement of chromatin structure during nucleotide excision repair (NER) was discovered more than 2 decades ago. However, the molecular basis of chromatin dynamics during NER remains undefined. Pioneering studies in the field of gene transcription have shown that ATP-dependent chromatin-remodeling complexes and histone-modifying enzymes play a critical role in chromatin dynamics during transcription. Similarly, recent studies have demonstrated that the SWI/SNF chromatin-remodeling complex facilitates NER both in vitro and in vivo. Additionally, histone acetylation has also been linked to the NER of ultraviolet light damage. In this article, we will discuss the role of these identified chromatin-modifying activities in NER.
Replicating chromatin: a tale of histonesThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.
Authors: Groth Anja
Published: February 2009

Chromatin serves structural and functional roles crucial for genome stability and correct gene expression. This organization must be reproduced on daughter strands during replication to maintain proper overlay of epigenetic fabric onto genetic sequence. Nucleosomes constitute the structural framework of chromatin and carry information to specify higher-order organization and gene expression. When replication forks traverse the chromosomes, nucleosomes are transiently disrupted, allowing the replication machinery to gain access to DNA. Histone recycling, together with new deposition, ensures reassembly on nascent DNA strands. The aim of this review is to discuss how histones — new and old — are handled at the replication fork, highlighting new mechanistic insights and revisiting old paradigms.
New developments in post-translational modifications and functions of histone H2A variantsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.
Authors: Thambirajah Anita A. , Li Andra , Ishibashi Toyotaka , Ausió Juan
Published: February 2009

Structural variability within histone families, such as H2A, can be achieved through 2 primary mechanisms: the expression of histone variants and the incorporation of chemical modifications. The histone H2A family contains several variants in addition to the canonical H2A forms. In this review, recent developments in the study of the heteromorphous variants H2A.X, H2A.Z, and macroH2A will be discussed. Particular focus will be given to the post-translational modifications (PTMs) of these variants, including phosphorylation, ubiquitination, acetylation, and methylation. The combination of the newly identified N- and C-terminal tail PTMs expands the multiplicity of roles that the individual H2A variants can perform. It is of additional interest that analogous sites within these different histone variants can be similarly modified. Whether this is a redundant function or a finely tuned one, designed to meet specific needs, remains to be elucidated.
ING function in apoptosis in diverse model systemsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.
Authors: Shah Sitar , Smith Heather , Feng Xiaolan , Rancourt Derrick E. , Riabowol Karl
Published: February 2009

Genetic studies in model organisms have shown that programmed cell death (apoptosis) plays a significant role during development, where a deficiency in apoptosis results in severe and diverse diseases. Dysregulation of apoptosis also contributes to a variety of human diseases, such as cancer and autoimmune diseases. ING family proteins (ING1–ING5) are involved in many cellular processes, and appear to play a significant role in apoptosis. Loss or downregulation of ING protein function is frequently observed in different tumour types, many of which are resistant to apoptosis, thus warranting their classification as type II tumour suppressors. Several different in vitro and in vivo models have explored the role of ING proteins in regulating apoptosis. In this review, we discuss the progress that has been made in understanding ING protein function in apoptosis using in vitro studies and Mus musculus, Xenopus laevis, and Caenorhabditis elegans experimental models, with an emphasis on ING1 and ING3.
Marks to stop the clock: histone modifications and checkpoint regulation in the DNA damage responseThis paper is one of a selection of papers published in this Special Issue, entitled 29th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.
Authors: Humpal Stephen E. , Robinson David A. , Krebs Jocelyn E.
Published: February 2009

DNA damage from endogenous and exogenous sources occurs throughout the cell cycle. In response to this damage, cells have developed a series of biochemical responses that allow them to recover from DNA damage and prevent mutations from being passed on to daughter cells. An important part of the DNA damage response is the ability to halt the progression of the cell cycle, allowing damaged DNA to be repaired. The cell cycle can be halted at semi-discrete times, called checkpoints, which occur at critical stages during the cell cycle. Recent work in our laboratory and by others has shown the importance of post-translational histone modifications in the DNA damage response. While many histone modifications have been identified that appear to facilitate repair per se, there have been surprisingly few links between these modifications and DNA damage checkpoints. Here, we review how modifications to histone H2A serine 129 (HSA129) and histone H3 lysine 79 (H3K79) contribute to the stimulation of the G1/S checkpoint. We also discuss recent findings that conflict with the current model of the way methylated H3K79 interacts with the checkpoint adaptor protein Rad9.
Histone acetylation: truth of consequences?This paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.
Authors: Choi Jennifer K. , Howe LeAnn J.
Published: February 2009

Eukaryotic DNA is packaged into a nucleoprotein structure known as chromatin, which is comprised of DNA, histones, and nonhistone proteins. Chromatin structure is highly dynamic, and can shift from a transcriptionally inactive state to an active form in response to intra- and extracellular signals. A major factor in chromatin architecture is the covalent modification of histones through the addition of chemical moieties, such as acetyl, methyl, ubiquitin, and phosphate groups. The acetylation of the amino-terminal tails of histones is a process that is highly conserved in eukaryotes, and was one of the earliest histone modifications characterized. Since its identification in 1964, a large body of evidence has accumulated demonstrating that histone acetylation plays an important role in transcription. Despite our ever-growing understanding of the nuclear processes involved in nucleosome acetylation, however, the exact biochemical mechanisms underlying the downstream effects of histone acetylation have yet to be fully elucidated. To date, histone acetylation has been proposed to function in 2 nonmutually exclusive manners: by directly altering chromatin structure, and by acting as a molecular tag for the recruitment of chromatin-modifying complexes. Here, we discuss recent research focusing on these 2 potential roles of histone acetylation and clarify what we actually know about the function of this modification.
The role of INI1/hSNF5 in gene regulation and cancerThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.
Authors: Stojanova Angelina , Penn Linda Z.
Published: February 2009

The precise modulation of chromatin dynamics is an essential and complex process that ensures the integrity of transcriptional regulation and prevents the transition of a normal cell into a cancerous one. ATP-dependent chromatin remodeling enzymes are multisubunit complexes that play a pivotal role in this operation through the mobilization of nucleosomes to promote DNA accessibility. Chromatin remodeling is mediated by the interaction of DNA-binding factors and individual members of this complex, directing its targeted recruitment to specific regulatory regions. In this review, we discuss a core subunit of the SWI/SNF ATP-dependent chromatin remodeling complex, known as INI1/hSNF5, in the context of transcriptional regulation and impact on cancer biology. In particular, we review current knowledge of the diverse protein interactions between INI1/hSNF5 and viral and cellular factors, with a special emphasis on the potent oncogene c-Myc.
Transcriptional and epigenetic functions of histone variant H2A.ZThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.
Authors: Draker Ryan , Cheung Peter
Published: February 2009

The chromatin organization of a genome ultimately dictates the gene expression profile of the cell. It is now well recognized that key mechanisms that regulate chromatin structure include post-translational modifications of histones and the incorporation of histone variants at strategic sites within the genome. H2A.Z is a variant of H2A that is localized to the 5′ end of many genes and is required for proper regulation of gene expression. However, its precise function in the transcription process is not yet well defined. In this review, we discuss some of the recent findings related to this histone variant, how it associates with other histone epigenetic marks, and how post-translational modifications of H2A.Z further define its function.
Structural and temporal regulation of centromeric chromatinThis paper is one of a selection of papers published in this Special Issue, entitled 29th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.
Authors: Mellone Barbara G.
Published: February 2009

Normal inheritance of genetic material requires that chromosomes segregate faithfully during mitosis and meiosis. The kinetochore is a unique structure that attaches chromosomes to the microtubule spindle, monitors proper chromosome attachment to the spindle through the mitotic checkpoint, and couples spindle and motor protein forces to move chromosomes during prometaphase and anaphase. The centromere is a specialized chromosomal site that is the structural and functional foundation for kinetochore formation, and is characterized by a unique type of chromatin that needs to be reconstituted after each replication cycle. In this review, recent progress in understanding the structural nature of this chromatin and how it is specifically maintained through cell division are discussed.
The multiple facets of histone H4-lysine 20 methylationThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.
Authors: Yang Hongbo , Mizzen Craig A.
Published: February 2009

Antisera raised against individual sites of histone post-translational modification (PTM) have provided critical insights into the biology of many of these PTMs. However, limitations inherent to immunochemical approaches can skew results obtained with these reagents, possibly leading investigators to misjudge the role of a specific histone PTM in a given process. We have used mass spectrometry in conjunction with cell synchronization, metabolic labeling, RNA interference, and other approaches to show that the SET domain proteins PR-Set7 and Suv4-20 mediate progressive global mono-, di-, and trimethylation of lysine 20 (K20) in newly synthesized histone H4, beginning approximately at the G2/M transition, well after new H4 is deposited in replicating chromatin during S phase. Immunochemical and other approaches have implicated H4-K20 methylation in multiple processes, including gene activation, gene repression, chromatin condensation, S phase progression, mitosis, and DNA-damage checkpoint signaling. Here, we review recent data on the regulation and significance of K20 methylation.
Consequences of climate change for biogeochemical cycling in forests of northeastern North AmericaThis article is one of a selection of papers from NE Forests 2100: A Synthesis of Climate Change Impacts on Forests of the Northeastern US and Eastern Canada.
Authors: Campbell John L. , Rustad Lindsey E. , Boyer Elizabeth W. , Christopher Sheila F. , Driscoll Charles T. , Fernandez Ivan J. , Groffman Peter M. , Houle Daniel , Kiekbusch Jana , Magill Alison H. , Mitchell Myron J. , Ollinger Scott V.
Published: February 2009

A critical component of assessing the impacts of climate change on forest ecosystems involves understanding associated changes in the biogeochemical cycling of elements. Evidence from research on northeastern North American forests shows that direct effects of climate change will evoke changes in biogeochemical cycling by altering plant physiology, forest productivity, and soil physical, chemical, and biological processes. Indirect effects, largely mediated by changes in species composition, length of growing season, and hydrology, will also be important. The case study presented here uses the quantitative biogeochemical model PnET-BGC to test assumptions about the direct and indirect effects of climate change on a northern hardwood forest ecosystem. Modeling results indicate an overall increase in net primary production due to a longer growing season, an increase in NO3–leaching due to large increases in net mineralization and nitrification, and slight declines in mineral weathering due to a reduction in soil moisture. Future research should focus on uncertainties, including the effects of (1) multiple simultaneous interactions of stressors (e.g., climate change, ozone, acidic deposition); (2) long-term atmospheric CO2enrichment on vegetation; (3) changes in forest species composition; (4) extreme climatic events and other disturbances (e.g., ice storms, fire, invasive species); and (5) feedback mechanisms that increase or decrease change.
Stand-replacing windthrow in the boreal forests of eastern Quebec
Authors: Bouchard Mathieu , Pothier David , Ruel Jean-Claude
Published: February 2009

The frequency of stand-replacing windthrow has rarely been evaluated over large spatio-temporal scales in boreal forests. This study examines stand-replacing windthrow that occurred within a forested area of 3 061 000 ha, both at the regional scale and at the scale of individual windthrow events. We specifically examined windthrow that covered at least 5 ha and for which mortality affected >75% of pre-windthrow canopy cover. At the regional scale, we found that windthrow affected, on average, 0.0255% of the area per year between 1971 and 2000. Logistic regressions indicate that stand age was the most important predictor variable at this scale, with severe windthrow less likely to occur in relatively young stands (<75 years). At the scale of individual windthrow events, slope direction was the most important predictor variable, with slopes facing the wind affected more. However, this factor was not significant at the regional scale probably because wind direction varied from one windthrow event to another. Overall, our results suggest that stand-replacing windthrow is difficult to predict and integrate into regional-scale forest management scenarios because it is primarily associated with the random occurrence of exceptional windstorms, while other biotic and abiotic variables play a relatively marginal role.
Nutrient cycling in two continuous cover scenarios for forest conversion of pine plantations on sandy soil. I. Nutrient cycling via aboveground tree biomass
Authors: De Schrijver A. , Geudens G. , Wuyts K. , Staelens J. , Gielis L. , Verheyen K.
Published: February 2009

Conversion of coniferous pine plantations into mixed-species forests on sandy soils is an important concern for forest and nature management in Europe. However, little is know of the effect of the applied sylvicultural strategy on biogeochemical cycling throughout the conversion process. This study examined the aboveground biomass production and nutrient (N, P, K, Ca, and Mg) cycling in terms of litterfall, immobilization in stems and branches, canopy exchange, and yearly root uptake in two scenarios of continuous cover forestry a decade after the first intervention for converting a homogeneous Scots pine (Pinus sylvestris L.) forest. Four regeneration types were studied: silver birch (Betula pendula L.) and pine after a shelterwood cutting and birch and pine after a group cutting. In conclusion, it can be stated that both the tree species and the conversion scenario influence the circulation of nutrients through the forest ecosystem: cycling of N, P, and K is determined by the tree species as well as the conversion scenario, whereas circulation of Ca and Mg is predominantly influenced by the type of conversion.
Growth, wood chemistry, and fibre length of Norway spruce in a long-term nutrient optimization experiment
Authors: Kaakinen Seija , Piispanen Riikka , Lehto Satu , Metsometsä Johanna , Nilsson Urban , Saranpää Pekka , Linder Sune , Vapaavuori Elina
Published: February 2009

The study was performed as part of a nutrient optimization experiment at Asa in southern Sweden. The experiment was established 1987, in a Norway spruce ( Picea abies (L.) Karst.) stand planted in 1975. In the nutrient optimization treatment (IL), all essential macro- and micronutrients were supplied, with irrigation water, every second day during the growing season. In October 2003, nine trees were harvested on both untreated control and IL plots. The IL treatment increased annual ring width during the first years of the experiment by ca. 30% and cumulative cross-sectional area 1.5-fold by the end of the experiment. Tracheid length was, however, not affected by the IL treatment. The nitrogen concentration of wood increased and starch concentration decreased as an effect of the IL treatment, suggesting that carbon was allocated to growth rather than storage. The IL treatment increased lignin concentration of wood by 3.4%. Chemical composition varied at different heights along the stem, but with no apparent trend.
Inferring the past from the present phylogeographic structure of North American forest trees: seeing the forest for the genes
Authors: Jaramillo-Correa Juan P. , Beaulieu Jean , Khasa Damase P. , Bousquet Jean
Published: February 2009

The study of past historical events that have led to ecological changes is a recurrent topic in many disciplines. Given that many of these events have left a large and long-lasting evolutionary imprint on the extant population genetic structure of species, phylogeographic studies on modern taxa have been largely used to infer the impacts of these events and to complement previous paleoecological and paleobotanical surveys. In spite of the geographical and geological complexity of North America, converging patterns can be observed when comparing the available genetic data for forest trees. Such patterns include the co-location of genetic discontinuities among species and their coincidence with mountain ranges (e.g., the Appalachians, the Rocky Mountains, the Sierra Nevada, or the Transverse Volcanic Belt) and with previously inferred glacial refugia. Using examples drawn from the available literature, we illustrate such shared features and present the contrasting phylogeographic patterns observed among the different regions of the continent. The various evolutionary consequences of historical events that can be deduced from these phylogeographic studies (e.g., past bottlenecks, founder effects, allopatric divergence, or introgressive hybridization) are additionally discussed. The present challenges and future research prospects that are likely to further advance this field are finally outlined.
Bordered pit and ray morphology involvement in elm resistance to Ophiostoma novo-ulmi
Authors: Martín Juan A. , Solla Alejandro , Esteban Luis G. , de Palacios Paloma , Gil Luis
Published: February 2009

The main objective of this study was to identify differential anatomical features between Ulmus pumila L. and Ulmus minor Mill. clones resistant to Dutch elm disease and U. minor clones susceptible to Dutch elm disease, with a focus on the intervascular pits and medullary rays. Resistant elms showed lower mean values than susceptible elms for pit membrane diameter, pit aperture area, pit membrane abundance per vessel-wall area, ray width, and ray tangential area. A principal component analysis of the parameters measured revealed slight differentiation between species but clearly grouped U. minor clones according to their susceptibility group. In comparison with susceptible elms, the pit structure observed in resistant elms may limit passive fungal spread within the sapflow, lower the probability of fungal cells passively reaching pit membranes, and reduce the vulnerability of the xylem to cavitation. Similarly, the ray structure observed in the resistant elms is likely to reduce the amount of easily accessible nutrients available for fungal growth as well as the rate of radial colonization in comparison with susceptible elms. Examination of the principal component loadings suggested that susceptible U. minor clones were mainly characterized by enhanced values of pit membrane abundance per vessel-wall area relative to resistant U. minor trees.
Competition dynamics in pure- versus mixed-family stands of loblolly and slash pine in the southeastern United States
Authors: Staudhammer Christina L. , Jokela Eric J. , Martin Timothy A.
Published: February 2009

Few studies within the native range of loblolly ( Pinus taeda L.) and slash pine ( Pinus elliottii Engelm. var. elliottii) have compared yield and stand dynamics in pure-family block versus mixed-family block plantings under a range of silvicultural treatments. Understanding intergenotypic competitive interactions is important for predicting phenotypic performance, defining growth strategies and ideotypes, and deploying the correct mix of families that possess complementary characteristics for enhanced yield and pest resistance. In 2000, replicated experimental trials were installed in the southeastern United States, controlling for genotype (pure- and mixed-family plantings; consisting of seven full-sibling loblolly and six full-sibling slash pine families), planting density (1334 vs. 2990 trees/ha), and levels of silvicultural treatment intensity (operational vs. intensive). We measured four installations of these trials. There were numerous examples of differential family performance in mixed versus pure plots manifested as significant deployment × family interactions for diameter at breast height, height, basal area, volume, survival, disease, and damage traits. Significant and consistent interactions of several families with mixed versus pure deployment led to the identification of putative crop and competition ideotypes in both loblolly and slash pine. Tree-level crown architectural traits and an index of growth efficiency for the identified families were consistent with the hypothesized ideotypes.