Molecular defects identified by whole exome sequencing in a child with Fanconi anemia

Fanconi anemia is a rare genetic disease characterized by bone marrow failure, multiple congenital malformations, and an increased susceptibility to malignancy. At least 15 genes have been identified that are involved in the pathogenesis of Fanconi anemia. However, it is still a challenge to assign the complementation group and to characterize the molecular defects in patients with Fanconi anemia. In the current study, whole exome sequencing was used to identify the affected gene(s) in a boy with Fanconi anemia. A recurring, non-synonymous mutation was found (c.3971C>T, p.P1324L) as well as a novel frameshift mutation (c.989_995del, p.H330LfsX2) in FANCA gene. Our results indicate that whole exome sequencing may be useful in clinical settings for rapid identification of disease-causing mutations in rare genetic disorders such as Fanconi anemia.     

Mutation c.359_363delGTATTinsATAC in the COL4A5 Causes alport syndrome in a Chinese family

The X-linked form of Alport syndrome is associated with mutations in the COL4A5 gene, which is located at Xq22.3 and encodes the α5 chain of type IV collagen. Here we clinically characterized a Chinese family with Alport Syndrome, but no ocular or hearing abnormalities have been observed in any patient in the family. Through Linkage analysis and direct DNA sequencing, a novel complex deletion/insertion mutation c.359_363delGTATTinsATAC in the COL4A5 gene was identified in the family. The mutation was found in all affected family members, but was not present in the unaffected family individuals or the 200 controls. The predicted mutant protein in the family is a truncated protein consisting of only 153 residues. Our report for the first time revealed that the frameshift mutation in the type IV collagen chain α5 causes only renal disease, without extrarenal lesion. Our study broadens genotypic and phenotypic spectrum of COL4A5 mutations associated with Alport syndrome.     

Genomics-based precision breeding approaches to improve drought tolerance in rice

Rice (Oryza sativa L.), the major staple food crop of the world, faces a severe threat from widespread drought. The development of drought-tolerant rice varieties is considered a feasible option to counteract drought stress. The screening of rice germplasm under drought and its characterization at the morphological, genetic, and molecular levels revealed the existence of genetic variation for drought tolerance within the rice gene pool. The improvements made in managed drought screening and selection for grain yield under drought have significantly contributed to progress in drought breeding programs. The availability of rice genome sequence information, genome-wide molecular markers, and low-cost genotyping platforms now makes it possible to routinely apply marker-assisted breeding approaches to improve grain yield under drought. Grain yield QTLs with a large and consistent effect under drought have been indentified and successfully pyramided in popular rice mega-varieties. Various rice functional genomics resources, databases, tools, and recent advances in “-omics” are facilitating the characterization of genes and pathways involved in drought tolerance, providing the basis for candidate gene identification and allele mining. The transgenic approach is successful in generating drought tolerance in rice under controlled conditions, but field-level testing is necessary. Genomics-assisted drought breeding approaches hold great promise, but a well-planned integration with standardized phenotyping is highly essential to exploit their full potential.     

A layover stop in the African American great migration: identity,ruination, and memory

Gone Home challenges dominant representations of Appalachia as white, placing in the foreground the life histories of African Americans who hail from the coalfields of eastern Kentucky. The book reveals how mass migration shapes subjectivities, examining two generations of African Americans who migrated into and out of the coalfields between 1910 and 1970. The coalfields were a layover stop in an intergenerational migration from the rural South to urban centres in the North, Midwest, and West. This review reflects on the significance of the layover stop, both empirically and conceptually. One of the key contributions of Gone Home is to show how the layover stop was important not only in terms of time and place, but also in terms of collective identity. The review concludes by reflecting on interconnected themes of industrial ruination and intergenerational memory.     

Objects on the loose

What happens to the relations involved in ownership when faced with new claims and challenges? This article looks at three examples of the way in which Mongolians are managing claims to resources and responding to new regimes of ownership. In each case, recourse to models of ownership based on masters and custodians are marshalled and extended to suit new contexts. I suggest that these should not be viewed as modern responses to the inequalities of current economic and social life [cf. Comaroff and Comaroff. 1999, May. Occult Economies and the Violence of Abstraction: Notes from the South African Postcolony. American Ethnologist, 26(2): 279–303], nor should they be viewed as a historical remnant from some previous social life. Rather, and here I follow Tsing [2004. Friction: An Ethnography of Global Connection. Princeton: Princeton University Press; 2015a. The Mushroom at the End of the World: On the Possibility of Life in Capitalist Ruins. Princeton: Princeton University Press; 2015b. Salvage Accumulation, or the Structural Effects of Capitalist Generativity. In Theorizing the Contemporary, Cultural Anthropology Website, March 30, 2015. https://culanth.org/fieldsights/656-salvage-accumulation-or-the-structural-effects-of-capitalist-generativity], they may be viewed as an outcome of an innovative ‘friction’, or ‘salvage economy’, between global and local realities that gives rise to what Gibson-Graham [2006. A Postcapitalist Politics. Minnesota: Minnesota University Press] argues is a heterogeneous capitalist landscape, here manifested in Mongolia’s dramatically rising and falling mineral economy.     

β‐Bulges: Extensive structural analyses of β‐sheets irregularities

β‐Sheets are quite frequent in protein structures and are stabilized by regular main‐chain hydrogen bond patterns. Irregularities in β‐sheets, named β‐bulges, are distorted regions between two consecutive hydrogen bonds. They disrupt the classical alternation of side chain direction and can alter the directionality of β‐strands. They are implicated in protein‐protein interactions and are introduced to avoid β‐strand aggregation. Five different types of β‐bulges are defined. Previous studies on β‐bulges were performed on a limited number of protein structures or one specific family. These studies evoked a potential conservation during evolution. In this work, we analyze the β‐bulge distribution and conservation in terms of local backbone conformations and amino acid composition. Our dataset consists of 66 times more β‐bulges than the last systematic study (Chan et al. Protein Science 1993, 2:1574–1590). Novel amino acid preferences are underlined and local structure conformations are highlighted by the use of a structural alphabet. We observed that β‐bulges are preferably localized at the N‐ and C‐termini of β‐strands, but contrary to the earlier studies, no significant conservation of β‐bulges was observed among structural homologues. Displacement of β‐bulges along the sequence was also investigated by Molecular Dynamics simulations.     

InDiaMed: A Comprehensive Database of Indian Medicinal plants for Diabetes

According to International Diabetes Federation (IDF), India has 62.4 million people with diabetes and by 2030 it is predicted that the number will rise to 100 million. Studies claim that there are around 410 experimentally proven Indian medicinal plants which have anti-diabetic activity, of which the mechanism of action of 109 plants has been elucidated or reported. So, the need of the hour is to explore the claims of Indian medicinal flora and open up the facets of many Indian plants which are being examined for their beneficial role in diabetes. So, we created a database (InDiaMed) of Indian medicinal plants that captures their role in anti-diabetic activity. InDiaMed''s features include chemical, pharmacological, biochemical and geographical information of the medicinal plant, scientifically relevant information of the plant, and the coherent research done on it in the field of diabetes. The database also includes the list of poly-herbal formulations which are used for treatment of diabetes in India.

Availability

http://www.indiamed.info     

Mercury uptake and phytotoxicity in terrestrial plants grown naturally in the Gumuskoy (Kutahya) mining area,Turkey

This study investigated mercury (Hg) uptake and transport from the soil to different plant parts by documenting the distribution and accumulation of Hg in the roots and shoots of 12 terrestrial plant species, all of which grow naturally in surface soils of the Gumuskoy Pb-Ag mining area. Plant samples and their associated soils were collected and analyzed for Hg content by ICP-MS. Mean Hg values in the soils, roots, and shoots of all plants were 6.914, 460, and 206 µg kg^?1, respectively and lower than 1. The mean enrichment factors for the roots (ECR) and shoots (ECS) of these plants were 0.06 and 0.09, respectively and lower than 1. These results show that the roots of the studied plants prevented Hg from reaching the aerial parts of the plants. The mean translocation factor (TLF) was 1.29 and higher than 1. The mean TLF values indicated that all 12 plant species had the ability to transfer Hg from the roots to the shoots but that transfer was more efficient in plants with higher ECR and ECS. Therefore, these plants could be useful for the biomonitoring of environmental pollution and for rehabilitating areas contaminated by Hg.