Effects of cultivar on rodent damage in Australian macadamia orchards

The Black rat (Rattus rattus), a serious pest of Australian macadamia orchards has been estimated to cause up to 30% crop damage in Australian orchards. In recent years an increase in the number of commercially available cultivars has seen a change in orchard characteristics in Australia, primarily effecting fruiting and flowering patterns. This has been suggested to affect the feeding behaviour of rodents and in turn altered the damage process. In this study we compare the extent of damage in orchards containing one of three prevalent cultivars (A4/A16, A268 and HAES 344/741) and investigate the influence of these cultivars, particularly their distinctive fruiting traits, on rodent damage within the orchard. We demonstrate that the temporal pattern and extent of damage differs between cultivar types. Newer Australian macadamia cultivars tested in this study were found to be far more susceptible to rodent damage than the older Hawaiian developed cultivars, most likely due to an extended fruiting period and thinner shells. This has resulted in a more sustained period of crop damage than the patterns of crop damage observed in previous Australian studies. Crop damage caused by R. rattus is significantly higher in orchards that maintain high levels of canopy resources through the fruiting season and we postulate that this is due to the extended fruiting periods of the new cultivars used. The maintenance of canopy resource load in turn corresponds to high crop damage, in this study resulting in crop losses of up to 25%.

The spatial distribution of rodent damage in Australian macadamia (Macadamia integrifolia) orchards

The Black Rat (Rattus rattus), a global pest within the macadamia production industry, causes up to 30% crop damage in Australian orchards. During early stages of production in Australia, research demonstrated the importance of non crop adjacent habitats as significant in affecting the patterns of crop damage seen throughout orchards. Where once rodent damage was limited to the outside edges of orchard blocks, growers are now reporting finding crop damage throughout entire orchards. This study therefore aims to explore the spatial patterns of rodent distribution and damage now occurring in Australian macadamia orchards. We show that rodent damage and rodent distribution in these newer production regions differ from that shown in previous Australian research. Previous Australian research has shown damage patterns which were associated with the edges of orchard blocks however this study demonstrates a more widespread damage distribution. In the current study there is no relationship between rodent damage and the orchard edge. Arboreal rodent nests were identified within these newer orchard systems, suggesting rodents are residing within the tree component of the orchard system and not dependent on adjacent non-crop habitat for shelter. Results from this study confirm that rodents have modified their nesting and foraging behaviour in newer orchards systems in Australia. We suggest that this is a response of increased and prolonged availability of macadamia nuts in newer production regions enabling populations to be maintained throughout the year. Management strategies will require modification if control is to be achieved.

Differences in membrane acyl phospholipid composition between an endothermic mammal and an ectothermic reptile are not limited to any phospholipid class

This study examined questions concerning differences in the acyl composition of membrane phospholipids that have been linked to the faster rates of metabolic processes in endotherms versus ectotherms. In liver, kidney, heart and brain of the ectothermic reptile, Trachydosaurus rugosus, and the endothermic mammal, Rattus norvegicus, previous findings of fewer unsaturates but a greater unsaturation index (UI) in membranes of the mammal versus those of the reptile were confirmed. Moreover, the study showed that the distribution of phospholipid head-group classes was similar in the same tissues of the reptile and mammal and that the differences in acyl composition were present in all phospholipid classes analysed, suggesting a role for the physical over the chemical properties of membranes in determining the faster rates of metabolic processes in endotherms. The most common phosphatidylcholine (PC) molecules present in all tissues (except brain) of the reptile were 16:0/18:1, 16:0/18:2, 18:0/18:2, 18:1/18:1 and 18:1/18:2, whereas arachidonic acid (20:4), containing PCs 16:0/ 20: 4, 18: 0/ 20: 4, were the common molecules in the mammal. The most abundant phosphatidylethanolamines ( PE) used in the tissue of the reptile were 18:0/18:2, 18:0/20:4, 18:1/18:1, 18:1/18:2 and 18:1/20:4, compared to 16: 0/ 18: 2, 16: 0/ 20: 4, 16: 0/ 22: 6, 18: 0/ 20: 4, 18: 0/ 22: 6 and 18:1/20: 4 in the mammal. UI differences were primarily due to arachidonic acid found in both PC and PEs, whereas docosahexaenoic acid (22:6) was a lesser contributor mainly within PEs and essentially absent in the kidney. The phospholipid composition of brain was more similar in the reptile and mammal compared to those of other tissues.

Common variants near ATM are associated with glycemic response to metformin in type 2 diabetes

Metformin is the most commonly used pharmacological therapy for type 2 diabetes. We report a genome-wide association study for glycemic response to metformin in 1,024 Scottish individuals with type 2 diabetes with replication in two cohorts including 1,783 Scottish individuals and 1,113 individuals from the UK Prospective Diabetes Study. In a combined meta-analysis, we identified a SNP, rs11212617, associated with treatment success (n = 3,920, P = 2.9 P×-9, odds ratio = 1.35, 95% CI 1.22-1.49) at a locus containing ATM, the ataxia telangiectasia mutated gene. In a rat hepatoma cell line, inhibition of ATM with KU-55933 attenuated the phosphorylation and activation of AMP-activated protein kinase in response to metformin. We conclude that ATM, a gene known to be involved in DNA repair and cell cycle control, plays a role in the effect of metformin upstream of AMP-activated protein kinase, and variation in this gene alters glycemic response to metformin. © 2011 Nature America, Inc. All rights reserved.

Genome-wide association study identifies susceptibility loci for open angle glaucoma at TMCO1 and CDKN2B-AS1

We report a genome-wide association study for open-angle glaucoma (OAG) blindness using a discovery cohort of 590 individuals with severe visual field loss (cases) and 3,956 controls. We identified associated loci at TMCO1 (rs4656461[G] odds ratio (OR) = 1.68, P = 6.1 × 10-10) and CDKN2B-AS1 (rs4977756[A] OR = 1.50, P = 4.7 × 10-9). We replicated these associations in an independent cohort of cases with advanced OAG (rs4656461 P = 0.010; rs4977756 P = 0.042) and two additional cohorts of less severe OAG (rs4656461 combined discovery and replication P = 6.00 × 10-14, OR = 1.51, 95% CI 1.35-1.68; rs4977756 combined P = 1.35 × 10-14, OR = 1.39, 95% CI 1.28-1.51). We show retinal expression of genes at both loci in human ocular tissues. We also show that CDKN2A and CDKN2B are upregulated in the retina of a rat model of glaucoma. © 2011 Nature America, Inc. All rights reserved.

An extravariation model for improving confidence intervals of population size estimates from removal data

We propose a new model for estimating the size of a population from successive catches taken during a removal experiment. The data from these experiments often have excessive variation, known as overdispersion, as compared with that predicted by the multinomial model. The new model allows catchability to vary randomly among samplings, which accounts for overdispersion. When the catchability is assumed to have a beta distribution, the likelihood function, which is refered to as beta-multinomial, is derived, and hence the maximum likelihood estimates can be evaluated. Simulations show that in the presence of extravariation in the data, the confidence intervals have been substantially underestimated in previous models (Leslie-DeLury, Moran) and that the new model provides more reliable confidence intervals. The performance of these methods was also demonstrated using two real data sets: one with overdispersion, from smallmouth bass (Micropterus dolomieu), and the other without overdispersion, from rat (Rattus rattus).

Classification of Nonenzymatic Homologues of Protein Kinases

Protein Kinase-Like Non-kinases (PKLNKs), which are closely related to protein kinases, lack the crucial catalytic aspartate in the catalytic loop, and hence cannot function as protein kinase, have been analysed. Using various sensitive sequence analysis methods, we have recognized 82 PKLNKs from four higher eukaryotic organisms, namely, Homo sapiens, Mus musculus, Rattus norvegicus, and Drosophila melanogaster. On the basis of their domain combination and function, PKLNKs have been classified mainly into four categories: (1) Ligand binding PKLNKs, (2) PKLNKs with extracellular protein-protein interaction domain, (3) PKLNKs involved in dimerization, and (4) PKLNKs with cytoplasmic protein-protein interaction module. While members of the first two classes of PKLNKs have transmembrane domain tethered to the PKLNK domain, members of the other two classes of PKLNKs are cytoplasmic in nature. The current classification scheme hopes to provide a convenient framework to classify the PKLNKs from other eukaryotes which would be helpful in deciphering their roles in cellular processes.

The role of competition and habitat in structuring small mammal communities in a tropical montane ecosystem in southern India

Small mammals were sampled in two natural habitats (montane stunted evergreen forests and montane grassland) and four anthropogenic habitats (tea, wattle, bluegum and pine plantation) in the Upper Nilgiris in southern India. Of the species trapped, eight were in montane evergreen forests and three were in other habitats. Habitat discrimination was studied in the rodents Rattus rattus and Mus famulus and the shrew Suncus montanus in the montane forest habitat. Multivariate tests on five variables (canopy cover, midstorey density, ground cover, tree density, canopy height) showed that R. rattus uses areas of higher tree density and lower canopy cover. Suncus montanus and M. famulus use habitat with higher tree density and ground cover and lower canopy height. Multivariate tests did not discriminate habitat use between the species. Univariate tests, however, showed that M. famulus uses areas of higher tree density than R. rattus and S. montanus. Rattus rattus was the dominant species in the montane forest, comprising 60.9% of total density, while the rodent Millardia meltada was the dominant species in the grassland. Studies of spatial interaction between these two species in habitats where they coexisted showed neither overlap nor avoidance between the species. Rattus rattus, however, did use areas of lower ground cover than did M. meltada. The analysis of spatial interactions between the species, habitat discrimination and use, and the removal experiments suggest that interspecific competition may not be a strong force in structuring these small mammal communities. There are distinct patterns in the use of different habitats by some species, but microhabitat selection and segregation is weak. Other factors such as intraspecific competition may play a more important role in these communities.

Expressão e distribuição de CGRP, VEGF e TGF-β na gengiva dos dentes de ratos com periodontite induzida por ligadura: aspectos imunohistoquímicos

No momento em que há a agressão tecidual e a defesa inata é deflagrada, mediadores químicos são liberados no local afetado. Esses mediadores podem ser de origem celular tais como CGRP, VEGF e TGFß. Os objetivos desta pesquisa foram avaliar a expressão e distribuição de CGRP, TGFß e VEGF na gengiva do primeiro molar inferior esquerdo de rato no 7 e 14 dias após a indução por ligadura; a expressão e distribuição de CGRP, TGFß e VEGF na gengiva do dente contralateral correspondente sem ligadura, no 7 e 14 dias, e se a indução da periodontite por ligadura no dente experimental provoca uma inflamação na gengiva do dente contralateral correspondente no 7 e 14 dias após a ligadura. Para o desenvolvimento deste trabalho foram selecionados 15 ratos Rattus Novergicus, Albinus, Wistar. O grupo experimental de 12 ratos foi dividido em 2 subgrupos compostos por 6 ratos cada um deles distribuídos da seguinte maneira: os do subgrupo A1 permaneceram com a ligadura no primeiro molar inferior esquerdo por 7 dias e foram sacrificados; os do subgrupo A-2 -permaneceram com a ligadura no primeiro molar inferior esquerdo por 14 dias e foram sacrificados. Outros três animais constituíram o grupo controle. Após o sacrifício dos 12 animais dos grupos experimentais e controle suas mandíbulas foram colocadas em ácido etilenodiaminotetracético (EDTA) neutro para sofrerem descalcificação. Então foram processadas para inclusão em parafina e os cortes histológicos foram corados pela hematoxilina-eosina e submetidos à técnica imunohistoquímica para imunomarcação de CGRP, VEGF e TGFß. Aos 7 dias de ligadura observou-se na lâmina própria gengival, epitélio juncional e epitélio oral, expressiva marcação para CGRP. A expressão de VEGF foi intensa na lamina própria e com pouca ou nenhuma marcação no epitélio oral e juncional. O TGFß apresentou pouca marcação na lâmina própria ou nenhuma marcação no epitélio oral e juncional. Aos 14 dias de ligadura houve expressiva marcação de CGRP na lâmina própria, epitélios oral e juncional. O VEGF e o TGFß apresentaram muita marcação na lâmina própria e pouca ou nenhuma marcação no epitélio oral e juncional. Na gengiva dos dentes contralaterais nos 7 e 14 dias houve pouca marcação do CGRP do TGFß na lâmina própria e muita marcação do VEGF. Na gengiva dos dentes controle observou-se muita marcação do CGRP no epitélio juncional e oral e na lâmina própria. O TGFß e o VEGF se expressaram muito pouco ou não se expressaram. Devido à marcação expressiva do VEGF na lâmina própria dos dentes contralaterais, permanece inconclusiva a adequação do uso dos dentes contralaterais nos estudos experimentais das doenças periodontais, embora a expressão de TGFß e CGRP tenham sido menores nestes dentes. A maior marcação do CGRP, VEGF e TGFß nos animais com 14 dias de ligadura do que aos 7 dias demonstra a progressão do processo inflamatório crônico, não se observando processo de reparação cicatricial.

Efeito do pré-condicionamento isquêmico remoto em modelo de lesão hepática por isquemia-reperfusão em ratos

A lesão por isquemia-reperfusão (I/R) é o mecanismo fisiopatológico central no desenvolvimento da insuficiência hepática pós-operatória. Diversas estratégias para minimizar suas consequências estão sendo desenvolvidas, mas ainda sem resultados satisfatórios. Recentemente o pré-condicionamento isquêmico remoto (PCIR), método em que ciclos breves de I/R aplicados em um órgão ou membro é capaz de atenuar os resultados da I/R em um órgão distante, vem sendo utilizado, em modelos experimentais, com resultados promissores. No entanto seu mecanismo de ação ainda não foi esclarecido. Um dos mecanismos propostos é a modulação na expressão das citocinas sintetizadas durante a resposta inflamatória que acompanha o processo de I/R. Foram utilizados 36 ratos (Rattus norvegicus), machos, com peso entre 250 e 280 g, divididos em três grupos: Grupo Sham, cirurgia simulada; Grupo IR, isquemia de 70% do fígado por 45 minutos e reperfusão; e Grupo PCIR, pré-condicionamento isquêmico remoto do fígado através de seis ciclos de isquemia-reperfusão da pata do animal, com quatro minutos de isquemia e quatro minutos de reperfusão em cada ciclo, seguido de isquemia hepática semelhante ao do Grupo IR. Terminado os procedimentos cirúrgicos, metade dos animais foi morta decorridos 60 minutos de reperfusão, e a outra metade após 180 minutos. Foi coletado tecido hepático do lobo submetido à isquemia, para estudo histopatológico, utilizando o índice de injúria hepática modificado; e sangue, para dosagem plasmática de TNF-α, IL-6, IL-10 e ALT. A análise histopatológica mostrou que a necrose celular foi significativamente reduzida no Grupo PCIR quando comparado com Grupo IR (p <0,0001). As transaminases mostraram o mesmo padrão com redução significativa dos seus valores no Grupo PCIR quando comparados com o Grupo I-R (p <0,0001). A dosagem das interleucinas mostrou redução significativa na expressão da IL-6 no Grupo PCIR quando comparado com o Grupo IR (p<0,001). Houve aumento da expressão de IL-10 nos grupo PCIR, porém não atingiu significância estatística. Não foi identificada diferença na dosagem de TNF-α nos grupos estudados. O PCI-R foi eficaz na redução na necrose celular resultante da lesão por I-R nos grupos estudados. A redução na síntese de IL-6 segue o padrão observado em outros estudos.

Molecular phylogeny and taxonomy of wood mice (genus Apodemus Kaup, 1829) based on complete mtDNA cytochrome b sequences, with emphasis on Chinese species

Phylogenetic relationships among 15 species of wood mice (genus Apodemus) were reconstructed to explore some long-standing taxonomic problems. The results provided support for the monophyly of the genus Apodemus, but could not reject the hypothesis of paraphyly for this genus. Our data divided the 15 species into four major groups: (1) the Sylvaemus group (A. sylvaticus, A. flavicollis, A. alpicola, and A. uralensis), (2) the Apodemus group (A. peninsulae, A. chevreri, A. agrarius, A. speciosus, A. draco, A. ilex, A. semotus, A. latronum, and A. mystacinus), (3) A. argenteus, and (4) A. gurkha. Our results also suggested that orestes should be a valid subspecies of A. draco rather than an independent species; in contrast, A. ilex from Yunnan may be regarded as a separate species rather than a synonym of orestes or draco. The species level status of A. latronum, tscherga as synonyms of A. uralensis, and A. chevrieri as a valid species and the closest sibling species of A. agrarius were further corroborated by our data. Applying a molecular clock with the divergences of Mus and Rattus set at 12 million years ago (Mya) as a calibration point, it was estimated that five old lineages (A. mystacinus and four major groups above) diverged in the late Miocene (7.82-12.74 Mya). Then the Apodemus group (excluding A. mystacinus) split into two subgroups: agrarius and draco, at about 7.17-9.95 Mya. Four species of the Sylvaemus group were estimated to diverge at about 2.92-5.21 Mya. The Hengduan Mountains Region was hypothesized to have played important roles in Apodemus evolutionary histories since the Pleistocene. (C) 2004 Elsevier Inc. All rights reserved.

Molecular cloning and responsive expression to injury stimulus of a defender against cell death 1 (DAD1) gene from bay scallops Argopecten irradians

Apoptosis is an active process of cell death, which is an integral part of growth and development in multicellular organisms. The defender against cell death 1 (DAD1), the regulatory protein to inhibit the apoptosis process, was first cloned from the bay scallop Argopecten irradians by randomly sequencing a whole tissue cDNA library and rapid amplification of cDNA end (RACE). The full-length cDNA of the A. irradians DAD1 was 607 bp, consist of a 5'-terminal untranslated region (UTR) of 63 bp, a 3'-terminal UTR of 205 bp with a canonical polyadenylation signal sequence AATAAA and a poly (A) tail, and an open reading frame of 339 bp. The deduced amino acid sequence of the A. irradians DAD1 showed 75.5% identity to Araneus ventricosus, 74.5% to Drosophila melanogaster, and 73.6% to Homo sapiens, Sus scrofa, Mesocricetus auratus, Rattus norvegicus and Mus musculus. Excluding the Saccharomyces cerevisiae DAD1 homologue, all animal DAD1 including A. irradians DAD1 homologue formed a subgroup and all plant DAD1 proteins formed another subgroup in the phylogenetic analysis. The A. irradians DAD1 was expressed in all examined tissues including adductor muscle, mantle, gills, digestive gland, gonad and hemolymph, suggesting that A. irradians DAD1 is expressed in most body tissues. Furthermore, the mRNA expression levels of A. irradians DAD1 gene of hemolymph were particularly high after injury, suggesting that the gene is responsive to injury stimuli.

栉孔扇贝C型凝集素-2(CfLec-2)基因的克隆和分析

栉孔扇贝是我国北方一种重要的贝类养殖品种。自1997年以来爆发的栉孔扇贝大规模死亡，给地区经济造成了重大损失并且已经严重威胁着扇贝养殖业的健康发展。然而，到目前为止，对扇贝免疫防御分子机理的了解还很少，深入研究扇贝免疫应答的分子机制是认识和了解病害发生和实现病害控制的重要途径。本研究采用了EST大规模测序和3’RACE的方法，从栉孔扇贝cDNA文库中克隆到一个凝集素基因CfLec-2，并对功能进行了研究。 CfLec-2 cDNA全长708bp，5’非翻译区(Untranslated Region, UTR)含有59bp，3’非翻译区含有163bp，具有典型的多聚腺苷酸加尾信号序列AATAAA和多聚腺苷酸尾巴，开放阅读框(Open Reading Frame, ORF )含有486bp，编码162个氨基酸残基，该多肽的理论分子量为16.8 kDa，等电点为4.54。利用SignalP分析，发现其信号肽的剪切位置在VEA-QSL之间。经BLASTP比对分析可知，CfLec-2基因编码的蛋白与人的Brevican，Anguilla japonica的C-type lectin-1和C-type lectin-2， Rattus norvegicus的CD23有较高的相似性，其中与Brevican的一致性有37%。Clustal W多序列比对发现该多肽具有标准长型C型凝集素所必须的6个保守半胱氨酸和相对保守的糖识别位点。用SMART(Small Modular Architecture Research Tool)软件分析发现其具有一个保守的糖识别结构域(Carbohydrate-recognition Domain, CRD)，氨基酸序列上第49、125、141、149位置上的半胱氨酸参与形成糖识别结构域，而位于N末端的第21和32位上的两个半胱胺酸形成额外的一个二硫键，位于115、116和117上的Glu、Pro、Asp则构成了糖识别位点。 将编码CfLec-2成熟肽段的cDNA序列克隆进pET32a(+)载体中，并在大肠杆菌Rosetta-gami(DE3)中重组表达CfLec-2。重组蛋白利用其具有的His tag纯化并复性后发现CfLec-2可以凝集溶血葡萄球菌，且凝集过程不需要钙离子的参与。并且，CfLec-2对大肠杆菌TOP10F’有微弱的抑菌活性，对溶壁微球菌、溶血葡萄球菌和鳗弧菌则没有抑菌活性。这一结果说明，CfLec-2可能不仅参与对入侵微生物的识别过程，而且可能作为效应分子起到了直接杀灭入侵微生物的作用。 本研究发现CfLec-2具有和以前在栉孔扇贝报道的CFLec-1完全不同的功 能，说明栉孔扇贝利用不同的凝集素来识别不同的病原，同时也暗示栉孔扇贝中可能有更多不同功能的凝集素有待发现。研究结果丰富和发展了海水无脊椎动物免疫学的内容，对进一步了解扇贝固有免疫的机制，实现养殖扇贝疾病防治具有重要参考价值。

Postnatal development of the retina in root vole Microtus oeconomus

Vision plays an important role in the living habits of animals, especially in feeding. We investigated the postnatal development of retina in root vole Microtus oeconornus. The result shows that the retina of the M. oeconornus is very primitive before postnatal day （PD） 3. The neuroblastic layer does not differentiate and makes up more than half of the retina layer. The outer plexiform layer （OPL） first comes into existence at PDS. At PD6, as the presence of the OPL becomes obvious, the outer nuclear layer （ONL） and inner nuclear layer （INL） are much clearer. At PD18, the retina is similar to an adult retina and each layer becomes distinct. The thickness and cell density of the ganglion cell layer （GCL） and ONL during different postnatal days were also examined. These results show that the thickness and density of ONL increase during ontogeny, while the thickness and density of GCL decrease. Compared with Rattus norvegicus, Apodemus agrarius , Cricetulus triton, Microtus mandarinus , Myospalax cansus , Spermophilus dauricus and Sciurotamias davidianus, the histological structure of the retina of M. oeconornus is between that of nocturnal and diurnal rodents.

高原鼠兔种群的性比

性比是反映动物种群的基本特征之一，因此成为种群生态学的主要研究内容。就种群的性比而言，在不同的物种、或同一物种在不同的时期和条件下都有极大的不同~[1-4]。性比的改变将影响动物的种群结构、家庭组成和交配关系，也影响动物两性的配偶竞争、繁殖投入、繁殖成功以及性二型的分化等~[4-13]。在繁殖过程中，动物可以采用改变性比的方法调节种群的密度和大小[2,14,15]。同时，动物的性比受多种因素的影响，不仅存在季节、年间以及地理变化的差异，而且受环境条件(如气温和降水量)的影响~[2～4]。捕食风险也是影响性比的主要因素。虽然许多动物出生时的性比是一样的，但是，由于捕食者在捕食猎物的过程中存在明显的选择性，使其性比发生了明显的变化~[16]。对于动物种群性比的研究已有诸多报道，其研究的动物包括海蛇尾(Ophiactis savignyi)~[5]、龙虾(Homarus gam- marus)~[6]、射毒蛙(Dendrobates purnilio)~[9]、斑马雀(Taeniopygyia guttata castanotis)~[8]、褐家鼠(Rattus norvegicus)~[17]等。高原鼠兔(Ochotona curzoniae)是青藏高原草地生态系统中的优势小哺乳类动物。有关高原鼠兔种群性比的研究，国内学者有过涉及~[18,19]，但所作工作多是在高原鼠兔繁殖生态学研究中进行的静态描述，对种群性比的年龄变化，季节和年度变化及其与环境条件的关系等方面的研究尚缺详细的报道。本文通过对高原鼠兔种群性比的年间比较、不同胎次性比的分析和越冬对其性比影响的研究，旨在探讨高原鼠兔的性比变化在其种群调节中的作用。