Loss of function of OsDCL1 affects microRNA accumulation and causes developmental defects in rice

MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are two types of noncoding RNAs involved in developmental regulation, genome maintenance, and defense in eukaryotes. The activity of Dicer or Dicer-like (DCL) proteins is required for the maturation of miRNAs and siRNAs. In this study, we cloned and sequenced 66 candidate rice (Oryza sativa) miRNAs out of 1,650 small RNA sequences (19 to approximately 25 nt), and they could be further grouped into 21 families, 12 of which are newly identified and three of which, OsmiR528, OsmiR529, and OsmiR530, have been confirmed by northern blot. To study the function of rice DCL proteins (OsDCLs) in the biogenesis of miRNAs and siRNAs, we searched genome databases and identified four OsDCLs. An RNA interference approach was applied to knock down two OsDCLs, OsDCL1 and OsDCL4, respectively. Strong loss of function of OsDCL1IR transformants that expressed inverted repeats of OsDCL1 resulted in developmental arrest at the seedling stage, and weak loss of function of OsDCL1IR transformants caused pleiotropic developmental defects. Moreover, all miRNAs tested were greatly reduced in OsDCL1IR but not OsDCL4IR transformants, indicating that OsDCL1 plays a critical role in miRNA processing in rice. In contrast, the production of siRNA from transgenic inverted repeats and endogenous CentO regions were not affected in either OsDCL1IR or OsDCL4IR transformants, suggesting that the production of miRNAs and siRNAs is via distinct OsDCLs.     

Effects of growth-promoting rhizobacteria on maize growth and rhizosphere microbial community under conservation tillage in Northeast China

Conservation tillage in conjunction with straw mulching is a sustainable agricultural approach. However, straw mulching reduces the soil temperature, inhibits early maize growth and reduces grain yield in cold regions. To address this problem, we investigated the effects of inoculation of plant growth-promoting rhizobacteria (PGPR) on maize growth and rhizosphere microbial communities under conservation tillage in Northeast China. The PGPR strains Sinorhizobium sp. A15, Bacillus sp. A28, Sphingomonas sp. A55 and Enterobacter sp. P24 were isolated from the maize rhizosphere in the same area and inoculated separately. Inoculation of these strains significantly enhanced maize growth, and the strains A15, A28 and A55 significantly increased grain yield by as much as 22%–29%. Real-time quantitative PCR and high-throughput sequencing showed that separate inoculation with the four strains increased the abundance and species richness of bacteria in the maize rhizosphere. Notably, the relative abundance of Acidobacteria_Subgroup_6, Chloroflexi_KD4-96, and Verrucomicrobiae at the class level and Mucilaginibacter at the genus level were positively correlated with maize biomass and yield. Inoculation with PGPR shows potential for improvement of maize production under conservation tillage in cold regions by regulating the rhizosphere bacterial community structure and by direct stimulation of plant growth.     

Sexual size dimorphism in a landlocked Pacific salmon in relation to breeding habitat features

Many animal species exhibit size dimorphism between sexes. Sexual selection, whereby male–male competition favors larger body sizes, has been considered a likely cause of sexual size dimorphism. Habitat features in breeding areas could affect the outcome of male–male competition, yet few attempts have been made to relate breeding habitat features with interpopulation variation in sexual size dimorphism. In this study, we examined interpopulation variation in sexual size dimorphism by studying the landlocked amago salmon (Oncorhynchus masou ishikawae) at a microgeographic scale. We found that female body size was independent of stream size but that male body size decreased with smaller stream sizes. A likely explanation is that the relationship between reproductive success and the size of males is influenced by the availability of refuges that are only available to small-bodied males. Sexual differences in body size increased with decreasing stream sizes, supporting the hypothesis that the reproductive success of larger males is reduced in smaller streams. In contrast, the maturation-length threshold increased with stream size for both sexes. The stream-size-based interpopulation variation in sexual size dimorphism and size at maturity in landlocked amago salmon may therefore have arisen through a combination of sexual and natural selection.     

Diet and Food Choice in Peruvian Red Uakaris (<Emphasis Type="Italic">Cacajao calvus ucayalii</Emphasis>): Selective or Opportunistic Seed Predation?

Even primates considered dietary specialists tend to eat a combination of fruit pulp, seeds, other plant parts, or animals. Specialist seed predators could either feed on seeds preferentially, or to avoid competition when ripe pulps are scarce. Pitheciin monkeys have specialized dentition that allows them to feed on seeds protected by hard shells, and the upper limit on the hardness of these is likely to be a function of jaw size. We recorded the diet of Peruvian red uakaris (Cacajao calvus ucayalii) on the Yavari River, Peru, to test the prediction that this seed predator would feed on the seeds of hard-shelled fruits preferentially over softer ones in relation to their availability in the forest. We also tested predictions that adult male, adult female, and juvenile diets would differ, with larger individuals eating more hard fruits. Uakaris ate 55.4% seeds, 38.9% pulps and arils, and 5.6% other items, but proportions varied through the year. More pulps, especially from the palm Mauritia flexuosa, were eaten when fruit availability was low, and more hard fruits were positively selected for than softer ones. Juveniles did not open the hardest fruit species opened by adults, and adult males ate harder fruits than females. These results provide evidence that seed eating in some primates has evolved beyond a means of avoiding competition for the ripe pulps typically preferred by many primates. Specialist seeding-eating primates therefore occupy divergent niches that require separate consideration from those of similar-sized primates.     

Interpreting expression profiles of cancers by genome-wide survey of breadth of expression in normal tissues

A critical and difficult part of studying cancer with DNA microarrays is data interpretation. Besides the need for data analysis algorithms, integration of additional information about genes might be useful. We performed genome-wide expression profiling of 36 types of normal human tissues and identified 2503 tissue-specific genes. We then systematically studied the expression of these genes in cancers by reanalyzing a large collection of published DNA microarray datasets. We observed that the expression level of liver-specific genes in hepatocellular carcinoma (HCC) correlates with the clinically defined degree of tumor differentiation. Through unsupervised clustering of tissue-specific genes differentially expressed in tumors, we extracted expression patterns that are characteristic of individual cell types, uncovering differences in cell lineage among tumor subtypes. We were able to detect the expression signature of hepatocytes in HCC, neuron cells in medulloblastoma, glia cells in glioma, basal and luminal epithelial cells in breast tumors, and various cell types in lung cancer samples. We also demonstrated that tissue-specific expression signatures are useful in locating the origin of metastatic tumors. Our study shows that integration of each gene's breadth of expression (BOE) in normal tissues is important for biological interpretation of the expression profiles of cancers in terms of tumor differentiation, cell lineage, and metastasis.     

Distribution of pathogenicity island markers and virulence factors in new phylogenetic groups of uropathogenic <Emphasis Type="Italic">Escherichia coli</Emphasis> isolates

The present study was aimed at investigating the relationship between the new Clermont’s phylogenetic groups, virulence factors, and pathogenicity island markers (PAIs) among uropathogenic Escherichia coli (UPEC) in Iran. This cross-sectional study was carried out on 140 UPEC isolates collected from patients with urinary tract infections in Bushehr, Iran. All isolates were subjected to phylogenetic typing using a new quadruplex-PCR method. The presence of PAI markers and virulence factors in UPEC strains was evaluated by multiplex PCR. The most predominant virulence gene was fimH (85%), followed by iucC (61.4%), papC (38.6%), hlyA (22.1%), cnf-1 (18.6%), afa (10.7%), papG and neuC (each 9.3%), ibeA (3.6%), and sfa/foc (0.7%). The most common phylogenetic group was related to B2 (39.3%), and the least common to A (0.7%). The most prevalent PAI marker was PAI IV536 (77.14%), while markers for PAI III536 (13.57%), PAI IIJ96 (12.86%), and PAI II536 (12.14%) were the least frequent among the UPEC strains. Meanwhile, the PAI IJ96 marker was not detected. There was a significant association between the phylogenetic group B2 and all the studied virulence genes and PAI markers. To our knowledge, this is the first study to compare the relationship between new phylogenetic groups, virulence genes and PAI markers in UPEC strains in Iran. The phylogenetic group B2 was predominantly represented among the studied virulence genes and PAI markers, indicating the preference of particular strains to carry virulence genes.     

The invasive herb <Emphasis Type="Italic">Lupinus polyphyllus</Emphasis> attracts bumblebees but reduces total arthropod abundance

Invasive plant species generally reduce the abundance and diversity of local plant species, which may translate into alterations at higher tropic levels, such as arthropods. Due to the diverse functional roles of arthropods in the ecosystems, it is critical to understand how arthropod communities are affected by plant invasions. Here, we investigated the impact of the invasive ornamental herb Lupinus polyphyllus (Lindl.) on arthropod communities during its main flowering period in southwestern Finland over two years. The total number of arthropods was about 46% smaller at the invaded sites than at the uninvaded sites in both study years, and this difference was mainly due to a lower abundance of beetles, Diptera, Lepidoptera, and ants. However, the number of bumblebees (particularly Bombus lucorum) was about twice as high at invaded sites compared with uninvaded sites, even though bumblebee richness did not differ between sites. There was no statistically significant difference between invaded and uninvaded sites in the abundances of the other arthropod groups considered (Hymenoptera (excluding bumblebees and ants), Hemiptera, and Arachnida). In addition, L. polyphyllus affected the relative abundance of four arthropod groups, with the order Lepidoptera being less common at invaded sites than at uninvaded sites, while the opposite was true for bumblebees, Hemiptera, and Arachnida. Overall, these results demonstrate that the negative impact of L. polyphyllus on biodiversity goes beyond its own trophic level, suggesting that this species has the potential to alter the abundance of different arthropod groups and, consequently, the structure of arthropod communities at a large scale.     

Alignment of molecular networks by integer quadratic programming

MOTIVATION: With more and more data on molecular networks (e.g. protein interaction networks, gene regulatory networks and metabolic networks) available, the discovery of conserved patterns or signaling pathways by comparing various kinds of networks among different species or within a species becomes an increasingly important problem. However, most of the conventional approaches either restrict comparative analysis to special structures, such as pathways, or adopt heuristic algorithms due to computational burden. RESULTS: In this article, to find the conserved substructures, we develop an efficient algorithm for aligning molecular networks based on both molecule similarity and architecture similarity, by using integer quadratic programming (IQP). Such an IQP can be relaxed into the corresponding quadratic programming (QP) which almost always ensures an integer solution, thereby making molecular network alignment tractable without any approximation. The proposed framework is very flexible and can be applied to many kinds of molecular networks including weighted and unweighted, directed and undirected networks with or without loops. AVAILABILITY: Matlab code and data are available from http://zhangroup.aporc.org/bioinfo/MNAligner or http://intelligent.eic.osaka-sandai.ac.jp/chenen/software/MNAligner, or upon request from authors. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

Surgical Decompression of Painful Diabetic Peripheral Neuropathy: The Role of Pain Distribution

Objective

To investigate the effect of surgical decompression on painful diabetic peripheral neuropathy (DPN) patients and discuss the role which pain distribution and characterization play in the management of painful DPN as well as the underlying mechanism involved.

Methods

A total of 306 patients with painful diabetic lower-extremity neuropathy were treated with Dellon surgical nerve decompression in our department. Clinical evaluation including Visual analogue scale (VAS), Brief Pain Inventory Short Form for diabetic peripheral neuropathy (BPI-DPN) questionnaire, two-point discrimination (2-PD), nerve conduction velocity (NCV) and high-resolution ultrasonography (cross-sectional area, CSA) were performed in all cases preoperatively, and at 6 month intervals for 2 years post-decompression. The patients who underwent surgery were retrospectively assigned into two subgroups (focal and diffuse pain) according to the distribution of the diabetic neuropathic pain. The control group included 92 painful DPN patients without surgery.

Results

The levels of VAS, scores in BPI-DPN, 2-PD, NCV results and CSA were all improved in surgical group when compared to the control group (P<0.05). More improvement of VAS, scores in BPI-DPN and CSA was observed in focal pain group than that in diffuse group (P<0.05).

Conclusions

Efficacy of decompression of multiple lower-extremity peripheral nerves in patients with painful diabetic neuropathy was confirmed in this study. While both focal and diffuse group could benefit from surgical decompression, pain relief and morphological restoration could be better achieved in focal group.