Rakesh K. Jain

Bio: Rakesh K. Jain is an academic researcher from Harvard University. The author has contributed to research in topics: Angiogenesis & Vascular endothelial growth factor. The author has an hindex of 200, co-authored 1467 publications receiving 177727 citations. Previous affiliations of Rakesh K. Jain include Government Medical College, Thiruvananthapuram & University of Oslo.

Guar gum as a gelling agent for plant tissue culture media

Abstract: Guar gum, a galactomannan derived from the endosperms of Cyamposis tetragonoloba, has been successfully used as a sole gelling agent for plant tissue culture media. Its suitability as a gelling agent was demonstrated by using guar gumgelled media for in vitro seed germination of Linum usitatissimum and Brassica juncea, in vitro axillary shoot proliferation in nodal explants of Crataeva nurvala, rooting of regenerated shoots of the same, in vitro androgenesis in anther cultures of Nicotiana tabacum, and somatic embryogenesis in callus cultures of Calliandra tweedii. The media used for these were gelled with either guar gum (2, 3, or 4%) or agar (0.9%). Guar gum-gelled media, like agar media, supported all these morphogenic responses. Rather, axillary shoot proliferation, rhizogenic and embryogenic responses were better on guar gum-gelled media than on agar media.

Role of oxygen vs. glucose in energy metabolism in a mammary carcinoma perfused ex vivo: direct measurement by 31P NMR

Abstract: The role of glycolysis vs. respiration in tumor energy metabolism has been studied, to date, primarily in vitro by using single cells, multicellular spheroids, or tissue slices. With the advent of in vivo NMR spectroscopy, several investigators have shown that tumor energy status depends on its blood flow. Since manipulation of blood flow alters both oxygen and glucose delivery to a solid tumor, these studies have not been able to separate the relative contribution of oxygen vs. glucose in energy metabolism in vivo. In the present study, we have overcome this problem by combining two methods: the tissue-isolated R3230AC mammary adenocarcinoma perfused ex vivo and 31P NMR spectroscopy. The isolated tumor permits one to control the perfusion pressure as well as the metabolite concentrations in the perfusate. NMR spectroscopy permits one to measure the ratio of nucleoside triphosphate to inorganic phosphate (NTP/Pi) and pH. Our results show that (i) the NTP/Pi ratio ex vivo is similar to that observed in vivo prior to surgery, (ii) the NTP/Pi ratio is insensitive to flow changes at high flow rates but is proportional to flow rate at flows comparable to those found in vivo, (iii) the NTP/Pi ratio of these tumors is resistant to hypoxia and is not maintained when glucose is removed or replaced with glutamine, and (iv) although both O2 and glucose are consumed by these tumors, the effect of perfusate flow rate appears to be mediated largely through glucose delivery. The current approach not only provides information about the role of glycolysis vs. respiration in a rodent tumor but also is general and versatile enough to provide similar data in human tumors perfused ex vivo.

Indigo production by naphthalene-degrading bacteria

Abstract: A wild-type naphthalene-degrading strain Pseudomonas putida RKJ1 and two recombinant strains each of Ps. putida and Escherichia coli carrying the genes for naphthalene degradation on a recombinant plasmid pRKJ3, produced indigo and indirubin pigments from indole. Naphthalene, salicylate and IPTG induced cells of naphthalene-degrading recombinant bacteria produced up to two times higher indigo compared with the uninduced cells. The maximum rates of indigo formation by Ps. putida RKJ1, Ps. putida RKJ5/pRKJ3, Ps. putida KT2442/pRKJ3, E. coli TB1/pRKJ3 and E. coli AB1157/pRKJ3 were 0.60, 0.80, 0.60, 1.20 and 1.50 nmol min-1 mg dry biomass-1, respectively, using indole as the substrate. The apparent Km values of indigo formation by these same bacteria were 0.22, 0.15, 0.10, 0. 21 and 0.20 mmol l-1, respectively, again using indole as the substrate. The present study revealed that E. coli AB1157 was the most efficient of the hosts tested for the expression of the plasmid encoded genes (pRKJ3) from the wild-type strain Ps. putida RKJ1. In addition, both recombinant E. coli strains were capable of producing indigo directly from nutrient medium.

Peptide Deformylase Inhibitors as Antibacterial Agents: Identification of VRC3375, a Proline-3-Alkylsuccinyl Hydroxamate Derivative, by Using an Integrated Combinatorial and Medicinal Chemistry Approach

Abstract: Although the study of microbial genomes has revealed an abundance of potentially useful targets, so far little has resulted from this much-heralded effort. Instead, most newly disclosed antibacterial agents target known enzymes that were identified through the use of classical biological methods. Witness the selection of posters recently presented at the “New Antimicrobial Agents and New Research Technology” section of the 42nd Interscience Conference on Antimicrobial Agents and Chemotherapy: 18 proteins were discussed as targets for antibacterial drug discovery; all of these were discovered through standard microbiology and biochemistry methods. One such target that has received much attention lately is the bacterial peptide deformylase (PDF) (EC 3.5.1.31). The protein synthesis processes for bacterial and mammalian cells are very similar. Both utilize the same amino acids and codons and share the same mechanism for elongation. However, a major difference between bacterial protein synthesis and mammalian cytosol protein synthesis is the use of formylmethionine as the initiator (19, 20). Unlike cytosol protein synthesis in mammalian cells, which is initiated with methionine, protein synthesis in bacteria is initiated with N-formylmethionine (2, 16), which is generated through enzymatic transformylation of methionyl-tRNA by formylmethionine tRNA transferase. The N-formyl methionine of the nascent protein in bacteria is removed by the sequential action of PDF and a methionine amino peptidase in order to afford the mature protein (2, 21). This formylation-deformylation cycle is essential for bacterial growth and is conserved among all studied bacterial species. Previous reports indicate that this cycle is not required for mammalian cells (for reviews, see references 7 and 31). The specific bacterial requirement for PDF in protein synthesis provides a rational basis for selectivity, making it an attractive drug discovery target. Although the in vitro development of bypass-resistant mutants in some bacterial organisms casts a shadow on the potential of using PDF inhibitors as antibacterial drugs, in vivo studies suggest that such mutants are much less virulent (for a detailed review, refer to Yuan et al. [31]). PDF activity was first reported by Adams in 1968 (1). This enzyme was not fully characterized until the early 1990s, when the Escherichia coli deformylase gene, def, was cloned (23) and when PDF was subsequently overproduced in E. coli (22, 23). Bacterial PDF utilizes a Fe2+ ion as the catalytic metal ion (8, 25, 26), but the ferrous ion in PDF is very unstable and can be quickly and irreversibly oxidized to the ferric species, resulting in an inactive enzyme (27). However, the ferrous ion can be replaced with a divalent nickel ion in vitro, resulting in much greater enzyme stability with little loss of enzyme activity (8). Since PDF is a metalloprotease, one possible approach to designing inhibitors consists of having a nonspecific chelating pharmacophore that binds to the catalytic metal ion and is coupled with a second moiety that binds to the active site, thus correctly positioning the chelator and providing the necessary selectivity and physicochemical properties. Such an approach has been successfully applied to the design of inhibitors of many other therapeutically important metalloproteases, the prime example being the angiotensin converting enzyme, followed more recently by the matrix metalloproteases (15). Recently, actinonin, a naturally occurring antibiotic with a hydroxamate moiety and a tripeptide binding domain, was shown to be a potent PDF inhibitor (5). Several three-dimensional studies of PDF-actinonin complexes suggest that the hydroxamate moiety of the inhibitor binds to and chelates the active center metal ion, while the tripeptide domain fits into the S1′-S3′ pocket of the enzyme (9). Using mechanistic information about the reaction catalyzed by PDF, together with an understanding of the general principles of metalloprotease inhibition, others have constructed several chelator-based inhibitor libraries according to the generic PDF inhibitor structure (Fig. ​(Fig.1)1) (31). In these libraries, X represents a chelating pharmacophore element that can bind to the metal ion at the active center of PDF, the N-butyl group mimics the methionine side chain, and P2′ and P3′ are domains of the inhibitor that can provide additional binding energy, selectivity, and favorable pharmacokinetic properties. These libraries were tested for PDF inhibition, antibacterial activity, and cytotoxicity. In this report, we describe the construction of such libraries, explore the inferred structure-activity relationships (SARs) of the resulting compounds, and report the subsequent identification of VRC3375, a unique PDF inhibitor-based broad-spectrum antibacterial agent with oral efficacy. FIG. 1. A generic PDF inhibitor structure. In the structure, X corresponds to a pharmacophore element capable of chelating metal ions. X attaches to a 2-substituted hexanoyl, which mimics the transition state of the hydrolysis of formyl-methionine.

A Safety and Survival Analysis of Neoadjuvant Bevacizumab with Standard Chemoradiation in a Phase I/II Study Compared with Standard Chemoradiation in Locally Advanced Rectal Cancer

Abstract: Introduction. Bevacizumab is increasingly being tested with neoadjuvant regimens in patients with localized cancer, but its effects on metastasis and survival remain unknown. This study examines the long-term outcome of clinical stage II/III rectal cancer patients treated in a prospective phase II study of bevacizumab with chemoradiation and surgery. As a benchmark, we used data from an analysis of 42 patients with locally advanced rectal cancer treated with a contemporary approach of preoperative fluoropyrimidine-based radiation therapy.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

Bevacizumab plus irinotecan, fluorouracil, and leucovorin for metastatic colorectal cancer

Abstract: background Bevacizumab, a monoclonal antibody against vascular endothelial growth factor, has shown promising preclinical and clinical activity against metastatic colorectal cancer, particularly in combination with chemotherapy. methods Of 813 patients with previously untreated metastatic colorectal cancer, we randomly assigned 402 to receive irinotecan, bolus fluorouracil, and leucovorin (IFL) plus bevacizumab (5 mg per kilogram of body weight every two weeks) and 411 to receive IFL plus placebo. The primary end point was overall survival. Secondary end points were progression-free survival, the response rate, the duration of the response, safety, and the quality of life. results The median duration of survival was 20.3 months in the group given IFL plus bevacizumab, as compared with 15.6 months in the group given IFL plus placebo, corresponding to a hazard ratio for death of 0.66 (P<0.001). The median duration of progressionfree survival was 10.6 months in the group given IFL plus bevacizumab, as compared with 6.2 months in the group given IFL plus placebo (hazard ratio for disease progression, 0.54; P<0.001); the corresponding rates of response were 44.8 percent and 34.8 percent (P=0.004). The median duration of the response was 10.4 months in the group given IFL plus bevacizumab, as compared with 7.1 months in the group given IFL plus placebo (hazard ratio for progression, 0.62; P=0.001). Grade 3 hypertension was more common during treatment with IFL plus bevacizumab than with IFL plus placebo (11.0 percent vs. 2.3 percent) but was easily managed. conclusions The addition of bevacizumab to fluorouracil-based combination chemotherapy results in statistically significant and clinically meaningful improvement in survival among patients with metastatic colorectal cancer.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.