Common variant in FUT2 gene is associated with levels of vitamin B12 in Indian population

Vitamin B₁₂ is an essential micronutrient synthesized by microorganisms. Mammals including humans have evolved ways for transport and absorption of this vitamin. Deficiency of vitamin B₁₂ (either due to low intake or polymorphism in genes involved in absorption and intracellular transport of this vitamin) has been associated with various complex diseases. Genome-wide association studies have recently identified several common single nucleotide polymorphisms (SNPs) in fucosyl transferase 2 gene (FUT2) to be associated with levels of vitamin B₁₂—the strongest association was with a non-synonymous SNP rs602662 in this gene. In the present study, we attempted to replicate the association of this SNP (rs602662) in an Indian population since a significant proportion has been reported to have low levels of vitamin B₁₂ in this population. A total of 1146 individuals were genotyped for this SNP using a single base extension method and association with levels of vitamin B₁₂ was assessed in these individuals. Regression analysis was performed to analyze the association considering various confounding factors like for age, sex, diet, hypertension, diabetes mellitus and coronary artery disease status. We found that the SNP rs602662 was significantly associated with the levels of vitamin B₁₂ (p value < 0.0001). We also found that individuals adhering to a vegetarian diet with GG (homozygous major genotype) have significantly lower levels of vitamin B₁₂ in these individuals. Thus, our study reveals that vegetarian diet along with polymorphism in the FUT2 gene may contribute significantly to the high prevalence of vitamin B₁₂ deficiency in India.     

Relatedness affects the density,distribution and phenotype of colonisers in four sessile marine invertebrates

Genetic diversity has emerged as an important source of variation in the ecological properties of populations, but there are few studies of genetic diversity effects on colonisation processes. This relative scarcity of studies is surprising given the influence of colonisation on species coexistence, invasion, and population persistence. Here, we manipulated relatedness in experimental populations of colonising larvae in four sessile marine invertebrates. We then examined the influence of coloniser relatedness on the number, spatial arrangement and phenotype of colonisers following permanent settlement. Overall, relatedness influenced colonisation in all four species, but the effects of relatedness on colonisation differed among species. The variable responses of species to manipulations of relatedness likely reflect differences in intensity of inter‐ and intra‐specific competition among adults, as well as the differential consequences of larval behaviours for each species. Relatedness appears to play an underappreciated role in the colonisation process, and we recommend that future studies of genetic diversity effects consider not only adult stages – the focus of most work to date – but also the importance of genetic diversity in early life history stages.     

Root system development of Lotus corniculatus L. in calcareous sands with embedded finer-textured fragments in an initial soil

Background and aims

In post mining landscapes as in the Lusatian region (Brandenburg, Germany), Pleistocene coarse-textured, sandy sediments are used for soil rehabilitation and land reclamation. The homogeneously-appearing initial soils are characterized by finer-textured soil clumps (fragments) of different sizes that are embedded in a sandy matrix. These soils with typical local-scale heterogeneity may serve as a model for studying how spatially-distributed soil fragments may be utilized by pioneering plant species. The aim of this study was to gain insight into the physical and chemical properties of sandy matrix and fragments that could possibly explain why embedded fragment may act as hot spots for root growth.

Methods

In 2009, three soil monoliths of dimension 50 cm?×?50 cm?×?50 cm that were exclusively vegetated by Lotus corniculatus L. planted in 2008 were studied. Each layer of 10 cm was sampled successively using a cubic metal frame with 10 cm edge length (25 samples per layer each with a volume of 1 l). The samples were analyzed for root biomass, root lengths and diameter, and for chemical and physical properties of sandy matrix and fragments.

Results

Bulk density, water contents, total carbon, total nitrogen, and plant available calcium contents were higher for the fragments compared to the sandy matrix. The roots of L. corniculatus were heterogeneously distributed in the monoliths. The root density distributions for the 1 L samples indicated a positive influence of fragments on directed root growth. Fragments embedded in the sandy matrix were found to be strongly penetrated by roots despite their relatively high bulk density. The presence of fragments also led to an increased root biomass in the sandy matrix in the direct vicinity of fragments. Such direct effects on root development were accompanied by more indirect effects by locally-elevated moisture and nutrient contents.

Conclusion

The results suggest that finer-textured fragments embedded in coarser-textured sediments, can have favorable effect on plant and root development during the initial stages of establishment of vegetation cover. The fragments can act as water and nutrient hot spots to improve supply of pioneering plants especially in coarse-textured soil. The existence of small-scale heterogeneities owing to incomplete sediment mixing e.g., in soil reclamation, could be generally important for controlling the speed and direction of early plants-establishment, for instance, in the succession of post-mining areas.     

Atypical Cohesin-Dockerin Complex Responsible for Cell Surface Attachment of Cellulosomal Components: BINDING FIDELITY,PROMISCUITY, AND STRUCTURAL BUTTRESSES*

The rumen bacterium Ruminococcus flavefaciens produces a highly organized multienzyme cellulosome complex that plays a key role in the degradation of plant cell wall polysaccharides, notably cellulose. The R. flavefaciens cellulosomal system is anchored to the bacterial cell wall through a relatively small ScaE scaffoldin subunit, which bears a single type IIIe cohesin responsible for the attachment of two major dockerin-containing scaffoldin proteins, ScaB and the cellulose-binding protein CttA. Although ScaB recruits the catalytic machinery onto the complex, CttA mediates attachment of the bacterial substrate via its two putative carbohydrate-binding modules. In an effort to understand the structural basis for assembly and cell surface attachment of the cellulosome in R. flavefaciens, we determined the crystal structure of the high affinity complex (K_d = 20.83 nm) between the cohesin module of ScaE (CohE) and its cognate X-dockerin (XDoc) modular dyad from CttA at 1.97-Å resolution. The structure reveals an atypical calcium-binding loop containing a 13-residue insert. The results further pinpoint two charged specificity-related residues on the surface of the cohesin module that are responsible for specific versus promiscuous cross-strain binding of the dockerin module. In addition, a combined functional role for the three enigmatic dockerin inserts was established whereby these extraneous segments serve as structural buttresses that reinforce the stalklike conformation of the X-module, thus segregating its tethered complement of cellulosomal components from the cell surface. The novel structure of the RfCohE-XDoc complex sheds light on divergent dockerin structure and function and provides insight into the specificity features of the type IIIe cohesin-dockerin interaction.     

Development of a new bioprocess scheme using frozen seed train intermediates to initiate CHO cell culture manufacturing campaigns

Agility to schedule and execute cell culture manufacturing campaigns quickly in a multi‐product facility will play a key role in meeting the growing demand for therapeutic proteins. In an effort to shorten campaign timelines, maximize plant flexibility and resource utilization, we investigated the initiation of cell culture manufacturing campaigns using CHO cells cryopreserved in large volume bags in place of the seed train process flows that are conventionally used in cell culture manufacturing. This approach, termed FASTEC (Frozen Accelerated Seed Train for Execution of a Campaign), involves cultivating cells to high density in a perfusion bioreactor, and cryopreserving cells in multiple disposable bags. Each run for a manufacturing campaign would then come from a thaw of one or more of these cryopreserved bags. This article reviews the development and optimization of individual steps of the FASTEC bioprocess scheme: scaling up cells to greater than 70 × 10⁶ cells/mL and freezing in bags with an optimized controlled rate freezing protocol and using a customized rack configuration. Flow cytometry analysis was also employed to understand the recovery of CHO cells following cryopreservation. Extensive development data were gathered to ensure that the quantity and quality of the drug manufactured using the FASTEC bioprocess scheme was acceptable compared to the conventional seed train process flow. The result of offering comparable manufacturing options offers flexibility to the cell culture manufacturing network. Biotechnol. Bioeng. 2013; 110: 1376–1385. © 2012 Wiley Periodicals, Inc.     

Cole Disease Results from Mutations in ENPP1

The coexistence of abnormal keratinization and aberrant pigmentation in a number of cornification disorders has long suggested a mechanistic link between these two processes. Here, we deciphered the genetic basis of Cole disease, a rare autosomal-dominant genodermatosis featuring punctate keratoderma, patchy hypopigmentation, and uncommonly, cutaneous calcifications. Using a combination of exome and direct sequencing, we showed complete cosegregation of the disease phenotype with three heterozygous ENPP1 mutations in three unrelated families. All mutations were found to affect cysteine residues in the somatomedin-B-like 2 (SMB2) domain in the encoded protein, which has been implicated in insulin signaling. ENPP1 encodes ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1), which is responsible for the generation of inorganic pyrophosphate, a natural inhibitor of mineralization. Previously, biallelic mutations in ENPP1 were shown to underlie a number of recessive conditions characterized by ectopic calcification, thus providing evidence of profound phenotypic heterogeneity in ENPP1-associated genetic diseases.     

The capacious hologenome

Blending disciplines can be transformative in science, yet interdisciplinary mergers should not escape healthy skepticism. Indeed, the history of biology shows us that debates about the relative importance of nuclear genetics vs. microbial symbiosis in eukaryotic biology are among the most engaging. Today's technology may help resolve this century old debate as it illuminates the interwoven genomics and functions of symbionts with their host genome. Thus, we can now assert that all subdisciplines of zoology require microbiology. Although controversial to some, the evidence from studies of host-associated microbial communities indicates that metazoans are hologenomes – interconnected compositions of animal and microbes.     

The emerging use of zebrafish to model metabolic disease

The zebrafish research community is celebrating! The zebrafish genome has recently been sequenced, the Zebrafish Mutation Project (launched by the Wellcome Trust Sanger Institute) has published the results of its first large-scale ethylnitrosourea (ENU) mutagenesis screen, and a host of new techniques, such as the genome editing technologies TALEN and CRISPR-Cas, are enabling specific mutations to be created in model organisms and investigated in vivo. The zebrafish truly seems to be coming of age. These powerful resources invoke the question of whether zebrafish can be increasingly used to model human disease, particularly common, chronic diseases of metabolism such as obesity and type 2 diabetes. In recent years, there has been considerable success, mainly from genomic approaches, in identifying genetic variants that are associated with these conditions in humans; however, mechanistic insights into the role of implicated disease loci are lacking. In this Review, we highlight some of the advantages and disadvantages of zebrafish to address the organism’s utility as a model system for human metabolic diseases.