巴基斯坦穆扎法拉巴德市Pattika公园鸟类多样性

2006年6月—2007年5月年对位于巴基斯坦自由克什米尔省穆扎法拉巴德市帕蒂卡(Pattika)休闲公园(EW:73°34′,纬度:NS:34°27′)内的栖息鸟类进行了调查,共有73种,分属10目35科。其中雀型目占73.55%,非雀型目占45%。其分布的多寡随该地区的季节而变化。大量物种出现在迁移繁殖的雨季。该公园处于人口密集之郊外,其间家畜的放养、灌木的砍伐及生境的干扰等人为因素都会对鸟类的分布和数量造成影响。     

Expression studies of stress responsive genes in cotton Gossypium hirsutum L.

Molecular Biology Reports - Cotton is the world’s richest source of natural fiber. Meanwhile cotton plant is top ranked stress sensitive plant thereby affecting its yield and fiber quality....     

Reducing the risk of false discovery enabling identification of biologically significant genome-wide methylation status using the HumanMethylation450 array

Background

The Illumina HumanMethylation450 BeadChip (HM450K) measures the DNA methylation of 485,512 CpGs in the human genome. The technology relies on hybridization of genomic fragments to probes on the chip. However, certain genomic factors may compromise the ability to measure methylation using the array such as single nucleotide polymorphisms (SNPs), small insertions and deletions (INDELs), repetitive DNA, and regions with reduced genomic complexity. Currently, there is no clear method or pipeline for determining which of the probes on the HM450K bead array should be retained for subsequent analysis in light of these issues.

Results

We comprehensively assessed the effects of SNPs, INDELs, repeats and bisulfite induced reduced genomic complexity by comparing HM450K bead array results with whole genome bisulfite sequencing. We determined which CpG probes provided accurate or noisy signals. From this, we derived a set of high-quality probes that provide unadulterated measurements of DNA methylation.

Conclusions

Our method significantly reduces the risk of false discoveries when using the HM450K bead array, while maximising the power of the array to detect methylation status genome-wide. Additionally, we demonstrate the utility of our method through extraction of biologically relevant epigenetic changes in prostate cancer.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-51) contains supplementary material, which is available to authorized users.     

Assessment of human–leopard conflict in Machiara National Park,Azad Jammu and Kashmir,Pakistan

Livestock depredation by leopards is one of the key conservation issues in landscapes with limited resources worldwide. Any attempts to mitigate human–leopard conflict and conserve the species in conflict should be based on an unequivocal understanding of the conflict patterns. A household survey was conducted with an intention to quantify livestock losses resulting from depredation by leopards in and around the Machiara National Park, Azad Jammu and Kashmir, Pakistan. A total of 301 livestock were killed between June 2007 and August 2008 by leopards. The extent of loss varied in different months, with maximum killing occurring in the month of May. Small-bodied livestock such as goats and sheep were more vulnerable than large-bodied cattle. Goats were killed in significantly higher numbers as compared to other livestock. Domestic animals were killed more frequently at night as compared to other times of the day. There was a significant effect of the nighttime protection measures on depredation. Most attacks happened in valleys and in areas far from the forests. Factors most closely associated with livestock depredation included decline of natural prey, herding practices, guarding especially during the nighttime, and repeated use of pastures where predators were known to be hunting actively. Attitudes of the local community towards leopards were largely negative, and further efforts should be made to improve support for carnivore conservation. We suggest widespread local community education and proactive human–leopard conflict management, particularly through adopting carnivore-friendly livestock protection measures.     

Synthesis of Antiviral Tetrahydrocarbazole Derivatives by Photochemical and Acid-catalyzed C-H Functionalization via Intermediate Peroxides (CHIPS)

The direct functionalization of C-H bonds is an important and long standing goal in organic chemistry. Such transformations can be very powerful in order to streamline synthesis by saving steps, time and material compared to conventional methods that require the introduction and removal of activating or directing groups. Therefore, the functionalization of C-H bonds is also attractive for green chemistry. Under oxidative conditions, two C-H bonds or one C-H and one heteroatom-H bond can be transformed to C-C and C-heteroatom bonds, respectively. Often these oxidative coupling reactions require synthetic oxidants, expensive catalysts or high temperatures. Here, we describe a two-step procedure to functionalize indole derivatives, more specifically tetrahydrocarbazoles, by C-H amination using only elemental oxygen as oxidant. The reaction uses the principle of C-H functionalization via Intermediate PeroxideS (CHIPS). In the first step, a hydroperoxide is generated oxidatively using visible light, a photosensitizer and elemental oxygen. In the second step, the N-nucleophile, an aniline, is introduced by Brønsted-acid catalyzed activation of the hydroperoxide leaving group. The products of the first and second step often precipitate and can be conveniently filtered off. The synthesis of a biologically active compound is shown.     

Autosomal Recessive Transmission of a Rare KRT74 Variant Causes Hair and Nail Ectodermal Dysplasia: Allelism with Dominant Woolly Hair/Hypotrichosis

Pure hair and nail ectodermal dysplasia (PHNED) comprises a heterogeneous group of rare heritable disorders characterized by brittle hair, hypotrichosis, onychodystrophy and micronychia. Autosomal recessive (AR) PHNED has previously been associated with mutations in either KRT85 or HOXC13 on chromosome 12p11.1-q14.3. We investigated a consanguineous Pakistani family with AR PHNED linked to the keratin gene cluster on 12p11.1 but without detectable mutations in KRT85 and HOXC13. Whole exome sequencing of affected individuals revealed homozygosity for a rare c.821T>C variant (p.Phe274Ser) in the KRT74 gene that segregates AR PHNED in the family. The transition alters the highly conserved Phe274 residue in the coil 1B domain required for long-range dimerization of keratins, suggesting that the mutation compromises the stability of intermediate filaments. Immunohistochemical (IHC) analyses confirmed a strong keratin-74 expression in the nail matrix, the nail bed and the hyponychium of mouse distal digits, as well as in normal human hair follicles. Furthermore, hair follicles and epidermis of an affected family member stained negative for Keratin-74 suggesting a loss of function mechanism mediated by the Phe274Ser substitution. Our observations show for the first time that homozygosity for a KRT74 missense variant may be associated with AR PHNED. Heterozygous KRT74 mutations have previously been associated with autosomal dominant woolly hair/hypotrichosis simplex (ADWH). Thus, our findings expand the phenotypic spectrum associated with KRT74 mutations and imply that a subtype of AR PHNED is allelic with ADWH.     

Comparative Study of Cr(VI) Removal by Exiguobacterium sp. in Free and Immobilized Forms

Cr(VI) is a toxic environmental pollutant. To determine the potential role of microbes towards chromate bioremediation, two bacterial strains, E1 and E4, that could tolerate Cr(VI) at levels up to 2250 μg ml^?1 were isolated from the soil of a tannery. They were identified as Exiguobacterium sp. To estimate the removal of Cr(VI) using immobilized bacterial cells, 2% sodium alginate and 2.5% agar were used as immobilizing matrices. In the case of sodium alginate, 89% and 93% of Cr(VI) removal by E1 and E4, respectively, were observed. When agar beads were used as an immobilizing matrix, removal was recorded as 39% and 48% for E1 and E4, respectively. Removal of Cr(VI) was also estimated in sterile and nonsterile tannery effluent. More Cr(VI) removal was noted in the nonsterile effluent than in the sterile effluent. The maximum uptake of Cr(VI) of bound cells of E1 and E4 was found to be 17.54 and 20.04 μg ml^?1, respectively. Fourier transform infrared (FTIR) spectra of cells of E4 with Cr(VI), without Cr(VI), and immobilized cells depicted several absorption peaks, mainly for P?OH group, C?H bending, C?O bond, and amide II groups, reflecting the complex nature of the bacterial cells and the contribution of these functional groups to the Cr(VI) binding process.     

A hAT superfamily transposase recruited by the cereal grass genome

Transposable elements are ubiquitous genomic parasites with an ancient history of coexistence with their hosts. A few cases have emerged recently where these genetic elements have been recruited for normal function in the host organism. We have identified an expressed hobo/Ac/Tam (hAT) family transposase-like gene in cereal grasses which appears to represent such a case. This gene, which we have called gary, is found in one or two copies in barley, two diverged copies in rice and two very similar copies in hexaploid wheat. No gary homologues are found in Arabidopsis. In all three cereal species, an apparently complete 2.5 kb transposase-like open reading frame is present and nucleotide substitution data show evidence for positive selection, yet the predicted gary protein is probably not an active transposase, as judged by the absence of key amino acids required for transposase function. Gary is expressed in wheat and barley spikes and gary cDNA sequences are also found in rice, oat, rye, maize, sorghum and sugarcane. The short inverted terminal repeats, flanked by an eight-nucleotide host sequence duplication, which are characteristic of a hAT transposon are absent. Genetic mapping in barley shows that gary is located on the distal end of the long arm of chromosome 2H. Wheat homologues of gary map to the same approximate location on the wheat group 2 chromosomes by physical bin-mapping and the more closely related of the two rice garys maps to the syntenic location near the bottom of rice chromosome 4. These data suggest that gary has resided in a single genomic location for at least 60 Myr and has lost the ability to transpose, yet expresses a transposase-related protein that is being conserved under host selection. We propose that the gary transposase-like gene has been recruited by the cereal grasses for an unknown function.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Conventional functional classification schemes underestimate the relationship with ecosystem functioning

Studies linking the functional diversity of a biota to ecosystem functioning typically employ a priori classifications of species into hypothetically complementary groups. However, multiple alternate classifications exist in which the number of functional groups, the number of species per functional group, and the grouping of species differ from the a priori scheme. Without assessing the relative precision, or ability of an a priori scheme to accurately predict ecosystem functioning relative to its many alternatives, the validity and utility of analyses based on a single a priori classification scheme remains unclear. We examine the precision of a priori classifications used in 10 experimental grassland systems in Europe and the United States that have found evidence for a significant role of functional plant diversity in governing ecosystem function. The predictive precision of the a priori classifications employed in these studies was seldom significantly higher than the precision of random classifications. Post-hoc classification schemes that performed well in predicting ecosystem function resembled each other more with regard to species composition than average classifications, but there was still considerable variability in the manner in which these classification schemes grouped species. These results suggest that we need a more nuanced understanding of how the diversity of functional traits of species in an assemblage affects ecosystem functioning.