Coimmobilized whole cells of Pseudomonas reptilivora and Micrococcus glutamicus in calcium alginate gel for the production of L-glutamic acid

A novel method of coimmobilized whole cells of Pseudomonas reptilivora and Micrococcus glutamicus, entrapped in calcium alginate beads have been used for the production of L-glutamic acid in a single stage fermentation process, using selected production medium enriched with glucose as substrate. The results obtained were compared with the L-glutamic acid production by free cells of Micrococcus glutamicus and by mixed culture of Pseudomonas reptilivora and Micrococcus glutamicus. The yield of glutamic acid obtained with mixed culture is relatively more than that the yield obtained with Micrococcus glutamicus alone. The properties of coimmobilized whole cells of Pseudomonas reptilivora and Micrococcus glutamicus in calcium alginate gel matrix have been investigated thoroughly and compared with those of free cells under most suitable conditions of fermentation.     

Changes in Blood-Brain Barrier Nutrient Transport in the Offspring of Iodine-Deficient Rats and Their Preventability

Thyroid hormones affect the structure and function of biological membranes. Whether or not they affect the Blood-Brain Barrier nutrient transport, the rate limiting membrane transport regulating nutrient supply to brain is to be established yet. That the impaired brain development and function seen in iodine deficiency could be due to such an effect has been assessed in situ by the brain uptake index (BUI) method in Wistar/NIN rat pups born to dams subjected to dietary iodine deficiency/rehabilitation for different times. Compared to controls (C), there was a significant decrease in the BUI values of 2-Deoxy-D-Glucose (2-DG) and L-leucine (Leu) in the pups (D1) born to dams chronically fed low iodine test (LIT) diet through their active growth and subsequent pregnancy and lactation. Surprisingly transport of L-Tyrosine (Tyr) and sucrose (the background marker) was not altered, nor was the BBB transport of all these nutrients affected by feeding LIT diet during the mothers' gestation (D2) and lactation (D3) only. The hypothyroidism in D1 pups was only moderate and preventable by rehabilitation of mothers with control diet from conception (R1) or parturition (R2), as were the changes in BBB nutrient transport. The results suggest that chronic material dietary iodine deficiency impairs BBB nutrient transport in the offspring and this could be prevented by their rehabilitation with iodine.     

Retroviral insertions in the VISION database identify molecular pathways in mouse lymphoid leukemia and lymphoma

AKXD recombinant inbred (RI) strains develop a variety of leukemias and lymphomas due to somatically acquired insertions of retroviral DNA into the genome of hematopoetic cells that can mutate cellular proto-oncogenes and tumor suppressor genes. We generated a new set of tumors from nine AKXD RI strains selected for their propensity to develop B-cell tumors, the most common type of human hematopoietic cancers. We employed a PCR technique called viral insertion site amplification (VISA) to rapidly isolate genomic sequence at the site of provirus insertion. Here we describe 550 VISA sequence tags (VSTs) that identify 74 common insertion sites (CISs), of which 21 have not been identified previously. Several suspected proto-oncogenes and tumor suppressor genes lie near CISs, providing supportive evidence for their roles in cancer. Furthermore, numerous previously uncharacterized genes lie near CISs, providing a pool of candidate disease genes for future research. Pathway analysis of candidate genes identified several signaling pathways as common and powerful routes to blood cancer, including Notch, E-protein, NFκB, and Ras signaling. Misregulation of several Notch signaling genes was confirmed by quantitative RT-PCR. Our data suggest that analyses of insertional mutagenesis on a single genetic background are biased toward the identification of cooperating mutations. This tumor collection represents the most comprehensive study of the genetics of B-cell leukemia and lymphoma development in mice. We have deposited the VST sequences, CISs in a genome viewer, histopathology, and molecular tumor typing data in a public web database called VISION (Viral Insertion Sites Identifying Oncogenes), which is located at . Keith C. Weiser and Bin Liu are authors that contributed equally to this work.     

Modifications of membrane lipids in response to wounding of Arabidopsis thaliana leaves

Mechanical wounding of Arabidopsis thaliana leaves results in modifications of most membrane lipids within 6 hours. Here, we discuss the lipid changes, their underlying biochemistry, and possible relationships among activated pathways. New evidence is presented supporting the role of the processive galactosylating enzyme SENSITIVE TO FREEZING2 in the wounding response.     

The regulation of TNFα production after heat and endotoxin stimulation is dependent on Annexin-A1 and HSP70

Febrile temperatures can induce stress responses which protect cells from damage and can reduce inflammation during infections and sepsis. However, the mechanisms behind the protective functions of heat in response to the bacterial endotoxin LPS are unclear. We have recently shown that Annexin-1 (ANXA1)-deficient macrophages exhibited higher TNFα levels after LPS stimulation. Moreover, we have previously reported that ANXA1 can function as a stress protein. Therefore in this study, we determined if ANXA1 is involved in the protective effects of heat on cytokine levels in macrophages after heat and LPS. Exposure of macrophages to 42 °C for 1 h prior to LPS results in an inhibition of TNFα production, which was not evident in ANXA1^−/− macrophages. We show that this regulation involves primarily MYD88-independent pathways. ANXA1 regulates TNFα mRNA stability after heat and LPS, and this is dependent on endogenous ANXA1 expression and not exogenously secreted factors. Further mechanistic studies revealed the possible involvement of the heat shock protein HSP70 and JNK in the heat and inflammatory stress response regulated by ANXA1. This study shows that ANXA1, an immunomodulatory protein, is critical in the heat stress response induced after heat and endotoxin stimulation.     

Anvaya: a workflows environment for automated genome analysis

Anvaya is a workflow environment for automated genome analysis that provides an interface for several bioinformatics tools and databases, loosely coupled together in a coordinated system, enabling the execution of a set of analyses tools in series or in parallel. It is a client-server workflow environment that has an advantage over existing software as it enables extensive pre & post processing of biological data in an efficient manner. "Anvaya" offers the user, novel functionalities to carry out exhaustive comparative analysis via "custom tools," which are tools with new functionality not available in standard tools, and "built-in PERL parsers," which automate data-flow between tools that hitherto, required manual intervention. It also provides a set of 11 pre-defined workflows for frequently used pipelines in genome annotation and comparative genomics ranging from EST assembly and annotation to phylogenetic reconstruction and microarray analysis. It provides a platform that serves as a single-stop solution for biologists to carry out hassle-free and comprehensive analysis, without being bothered about the nuances involved in tool installation, command line parameters, format conversions required to connect tools and manage/process multiple data sets at a single instance.     

Cloning and sequencing of a full-length rat sucrase-isomaltase-encoding

Sucrase-isomaltase (SI) has been widely used as a marker enzyme to study cellular differentiation in the small intestine. We isolated a 6.1-kb SI cDNA clone (GC1.4) from a size-fractionated cDNA library from rat intestine. Sequencing of this cDNA clone showed 6066 nucleotides (nt) with an open reading frame (ORF) of 1841 amino acids (aa). The nt sequence correctly predicts several known aa stretches in the protein. The deduced aa sequence showed 78 and 75% overall identity with the rabbit and human SI, respectively. At the active sites of both S and I, the rat nt sequence encodes stretches of 14 and 16 aa, respectively, which show 100% identity to rabbit and human SI. In the region immediately beyond the transmembrane domain, the rat sequence encodes an extra 10 aa, as compared to rabbit and human. This 10-aa insertion consists almost entirely of Pro, Ser and Thr, and may be responsible for additional 0-glycosylations of rat SI. The cDNA contains a 3'-UTR (untranslated region) of 499 nt with polyadenylation signal sequence and a poly(A) tract. The ATG start codon was found 41 nt downstream from the 5' end of the cDNA. Primer extension experiments showed the cap site to be 61 nt upstream from the start codon. The results indicate that our cDNA clone lacks only 20 nt in the 5'-UTR. Given that this cDNA encodes the entire coding region of SI, it should be useful in elucidating the regulatory mechanisms of SI biosynthesis, localization and targeting during rat intestinal development and differentiation.