Extreme clonality in lymphoblastoid cell lines with implications for allele specific expression analyses

Lymphoblastoid cell lines (LCL) are being actively and extensively used to examine the expression of specific genes and genome-wide expression profiles, including allele specific expression assays. However, it has recently been shown that approximately 10% of human genes exhibit random patterns of monoallelic expression within single clones of LCLs. Consequently allelic imbalance studies could be significantly compromised if bulk populations of donor cells are clonal, or near clonal. Here, using X chromosome inactivation as a readout, we confirm and quantify widespread near monoclonality in two independent sets of cell lines. Consequently, we recommend where possible the use of bulk, non cell line, ex vivo cells for allele specific expression assays.     

北方牧区草地资源分类经营机制与可持续发展

草地是畜牧业生产和生态保护的重要资源.在短期经济利益的驱动下造成北方牧区草地大面积退化和荒漠化、生产力下降、自我恢复能力降低、水土流失加剧和涵养功能减弱,对牧区经济发展、社会稳定和生态安全构成了威胁,严重影响着草地畜牧业的可持续发展.以新疆阿勒泰为例,依据草地资源的生产经济性能、生态服务价值重要性和季节放牧利用特征,构建了基于GIS 技术的草地生产力指数、草地生态服务价值指数和草地资源分类经营的功能分区模型,建立以主导功能和时空格局为主的草地资源分类经营调控机制,将阿勒泰牧区的草地从空间上划分为经济功能区、混合功能区和生态功能区.结果表明:(1)经济功能区,以获取最大的经济效益为目的,面积约648.69万hm2,占总可利用草地面积的65.8%,主要分布在平原荒漠;(2)生态功能区,以生态保护和社会效益为目的,面积约136.4万hm2,占总可利用草地面积的13.9%,主要分布在平原荒漠草原、山地草原、高寒草甸;(3)混合功能区,在适度利用条件下,生态效益与经济效益并重,面积约200.1万hm2,占总可利用草地面积的20.3%,主要分布在山地草原化荒漠、山地草甸草原、平地草甸、山地荒漠草原、山地草甸和高寒草原.通过对草地资源的分类经营,将畜牧业生产重心转向经济功能区,转移生态功能区的放牧家畜,减轻混合功能区的放牧压力,形成草地资源在功能、系统、时序和空间的耦合结构,实现牧区草地资源利用的可持续发展.     

Validation of reference genes for the relative quantification of gene expression in human epicardial adipose tissue

Background

Relative quantification is a commonly used method for assessing gene expression, however its accuracy and reliability is dependent upon the choice of an optimal endogenous control gene, and such choice cannot be made a priori. There is limited information available on suitable reference genes to be used for studies involving human epicardial adipose tissue. The objective of the current study was to evaluate and identify optimal reference genes for use in the relative quantification of gene expression in human epicardial fat depots of lean, overweight and obese subjects.

Methodology/Principal Findings

Some of the commonly used reference genes including 18S, ACTB, RPL27, HPRT, CYCA, GAPDH, RPLPO, POLR2A and B2M were quantified using real-time PCR analysis. The expression stability of these genes was evaluated using Genorm, Normfinder and Bestkeeper algorithms. In addition, the effect of sample size on the validation process was studied by randomly categorizing subjects in two cohorts of n = 2 and n = 33.

Conclusions/Significance

CYCA, GAPDH and RPL27 were identified as the most stable genes common to all three algorithms and both sample sizes. Their use as reference gene pairs might contribute to the enhanced robustness of relative quantification in the studies involving the human epicardial adipose tissue.     

云南黑颈长尾雉(Syrmaticus humiae)分布及栖息地类型调查

黑颈长尾雉是鸡形目鸟类中的濒危物种,分布局限于印度东北部、缅甸北部、泰国西北部和中国西南部。在中国,该雉仅栖息于广西西部和云南中部、西部及南部地区。１９９２年至１９９５年在云南对黑颈长尾雉的分布及栖息生境进行了专门的调查,共有１３县１８个地点记录到黑颈长尾雉分布。通过访问还获得一些可能有黑颈长尾雉分布但需进一步证实的地点。黑颈长尾雉在云南的栖息生境主要有热带季雨林、亚热带常绿阔叶林、暖温性针叶林、暖热性针叶林和落叶阔叶林等５种类型。栖息地丧失和高强度狩猎是导致黑颈长尾雉濒危的主要原因,如欲有效保护该物种,不仅要注意保护其栖息地,更要严格控制非法狩猎。     

Allelopathy of plasmid-bearing and plasmid-free organisms competing for two complementary resources in a chemostat

We consider a model of competition between plasmid-bearing and plasmid-free organisms for two complementary nutrients in a chemostat. We assume that the plasmid-bearing organism produces an allelopathic agent at the cost of its reproductive abilities which is lethal to plasmid-free organism. Our analysis leads to different thresholds in terms of the model parameters acting as conditions under which the organisms associated with the system cannot thrive even in the absence of competition. Local stability of the system is obtained in the absence of one or both the organisms. Also, global stability of the system is obtained in the presence of both the organisms. Computer simulations have been carried out to illustrate various analytical results.     

Allelopathy of plasmid-bearing and plasmid-free organisms competing for two complementary resources in a chemostat

We consider a model of competition between plasmid-bearing and plasmid-free organisms for two complementary nutrients in a chemostat. We assume that the plasmid-bearing organism produces an allelopathic agent at the cost of its reproductive abilities which is lethal to plasmid-free organism. Our analysis leads to different thresholds in terms of the model parameters acting as conditions under which the organisms associated with the system cannot thrive even in the absence of competition. Local stability of the system is obtained in the absence of one or both the organisms. Also, global stability of the system is obtained in the presence of both the organisms. Computer simulations have been carried out to illustrate various analytical results.     

甘肃省动植物资源现状及可持续发展对策

甘肃地处中国的中部偏北，位于黄土高原、内蒙古高原和 藏高原的交汇处，是我另唯一横跨三大自然区的 分。全省的动植物资源极春丰富。据不完全调查，共有脊椎动物９２４种和亚种，占国内４８６５种１９．０１％，种子植物３８６７种，占国内３００００种的１２．９％。由于生态环境破坏，乱捕滥猎，使动植物相断消失，许多国家级保护的动植物成为濒危物种。为保护生态环境，实现可持续发展，本文提出了５项持续利用的对策：１）加     

Design of reference populations for genomic selection in crossbreeding programs

Background

In crossbreeding programs, genomic selection offers the opportunity to make efficient use of information on crossbred (CB) individuals in the selection of purebred (PB) candidates. In such programs, reference populations often contain genotyped PB animals, although the breeding objective is usually more focused on CB performance. The question is what would be the benefit of including a larger proportion of CB individuals in the reference population.

Methods

In a deterministic simulation study, we evaluated the benefit of including various proportions of CB animals in a reference population for genomic selection of PB animals in a crossbreeding program. We used a pig breeding scheme with selection for a moderately heritable trait and a size of 6000 for the reference population.

Results

Applying genomic selection to improve the performance of CB individuals, with a genetic correlation between PB and CB performance (r_PC) of 0.7, selection accuracy of PB candidates increased from 0.49 to 0.52 if the reference population consisted of PB individuals, it increased to 0.55 if the reference population consisted of the same number of CB individuals, and to 0.60 if the size of the CB reference population was twice that of the reference population for each PB line. The advantage of using CB rather than PB individuals increased linearly with the proportion of CB individuals in the reference population. This advantage disappeared quickly if r_PC was higher or if the breeding objective put some emphasis on PB performance. The benefit of adding CB individuals to an existing PB reference population was limited for high r_PC.

Conclusions

Using CB rather than PB individuals in a reference population for genomic selection can provide substantial advantages, but only when correlations between PB and CB performances are not high and PB performance is not part of the breeding objective.     

Verification of reference genes for relative quantification of gene expression by real-time reverse transcription PCR in the pig

The aim of this study was to develop a set of reliable reference genes for quantification of mRNA expression in the pig. The mRNA expression stability in pig tissues was studied for 4 genes:EEF1A1, GAPDH, HPRT1 andTOP2B. The level of expression was characterized byCt values for each gene and each tissue. By using the geNorm algorithm, the stability of the reference genes was determined in the diaphragm, heart, kidney, liver, lungs, longissimus muscle, and spleen. On the basis of this information, suitable reference genes can be selected for mRNA expression studies in relevant pig tissues.     

Alternative enzymes as a special strategy for the adaptation of procaryotic organisms (Review)

The literature data on prokaryotic adaptation to changes in environmental conditions that lead to a change in the metabolism and, at the same time, are also exhibited in the preservation of many biochemical reactions of the central metabolism due to the functioning of alternative enzymes are summarized. Unlike isozymes, the alternative enzymes have different active sites and are encoded by different genes but catalyze the same key biochemical reaction of the central metabolism. Biochemical inconstancy and the immutability of a biochemical reaction in prokaryotes should be taken into account in metabolic engineering aimed at optimization of gene expression.