SDF-1 activates papillary label-retaining cells during kidney repair from injury

The adult kidney contains a population of low-cycling cells that resides in the papilla. These cells retain for long periods S-phase markers given as a short pulse early in life; i.e., they are label-retaining cells (LRC). In previous studies in adult rat and mice, we found that shortly after acute kidney injury many of the quiescent papillary LRC started proliferating (Oliver JA, Klinakis A, Cheema FH, Friedlander J, Sampogna RV, Martens TP, Liu C, Efstratiadis A, Al-Awqati Q. J Am Soc Nephrol 20: 2315-2327, 2009; Oliver JA, Maarouf O, Cheema FH, Martens TP, Al-Awqati Q. J Clin Invest 114: 795-804, 2004) and, with cell-tracking experiments, we found upward migration of some papillary cells including LRC (Oliver JA, Klinakis A, Cheema FH, Friedlander J, Sampogna RV, Martens TP, Liu C, Efstratiadis A, Al-Awqati Q. J Am Soc Nephrol 20: 2315-2327, 2009). To identify molecular cues involved in the activation (i.e., proliferation and/or migration) of the papillary LRC that follows injury, we isolated these cells from the H2B-GFP mice and found that they migrated and proliferated in response to the cytokine stromal cell-derived factor-1 (SDF-1). Moreover, in a papillary organ culture assay, the cell growth out of the upper papilla was dependent on the interaction of SDF-1 with its receptor Cxcr4. Interestingly, location of these two proteins in the kidney revealed a complementary location, with SDF-1 being preferentially expressed in the medulla and Cxcr4 more abundant in the papilla. Blockade of Cxcr4 in vivo prevented mobilization of papillary LRC after transient kidney ischemic injury and worsened its functional consequences. The data indicate that the SDF-1/Cxcr4 axis is a critical regulator of papillary LRC activation following transient kidney injury and during organ repair.     

Deciphering the genetic architecture and ethnographic distribution of IRD in three ethnic populations by whole genome sequence analysis

Patients with inherited retinal dystrophies (IRDs) were recruited from two understudied populations: Mexico and Pakistan as well as a third well-studied population of European Americans to define the genetic architecture of IRD by performing whole-genome sequencing (WGS). Whole-genome analysis was performed on 409 individuals from 108 unrelated pedigrees with IRDs. All patients underwent an ophthalmic evaluation to establish the retinal phenotype. Although the 108 pedigrees in this study had previously been examined for mutations in known IRD genes using a wide range of methodologies including targeted gene(s) or mutation(s) screening, linkage analysis and exome sequencing, the gene mutations responsible for IRD in these 108 pedigrees were not determined. WGS was performed on these pedigrees using Illumina X10 at a minimum of 30X depth. The sequence reads were mapped against hg19 followed by variant calling using GATK. The genome variants were annotated using SnpEff, PolyPhen2, and CADD score; the structural variants (SVs) were called using GenomeSTRiP and LUMPY. We identified potential causative sequence alterations in 61 pedigrees (57%), including 39 novel and 54 reported variants in IRD genes. For 57 of these pedigrees the observed genotype was consistent with the initial clinical diagnosis, the remaining 4 had the clinical diagnosis reclassified based on our findings. In seven pedigrees (12%) we observed atypical causal variants, i.e. unexpected genotype(s), including 4 pedigrees with causal variants in more than one IRD gene within all affected family members, one pedigree with intrafamilial genetic heterogeneity (different affected family members carrying causal variants in different IRD genes), one pedigree carrying a dominant causative variant present in pseudo-recessive form due to consanguinity and one pedigree with a de-novo variant in the affected family member. Combined atypical and large structural variants contributed to about 20% of cases. Among the novel mutations, 75% were detected in Mexican and 50% found in European American pedigrees and have not been reported in any other population while only 20% were detected in Pakistani pedigrees and were not previously reported. The remaining novel IRD causative variants were listed in gnomAD but were found to be very rare and population specific. Mutations in known IRD associated genes contributed to pathology in 63% Mexican, 60% Pakistani and 45% European American pedigrees analyzed. Overall, contribution of known IRD gene variants to disease pathology in these three populations was similar to that observed in other populations worldwide. This study revealed a spectrum of mutations contributing to IRD in three populations, identified a large proportion of novel potentially causative variants that are specific to the corresponding population or not reported in gnomAD and shed light on the genetic architecture of IRD in these diverse global populations.     

A novel one-pot de-blocking and conjugation reaction step leads to process intensification in the manufacture of PEGylated insulin IN-105

Bio-catalytic in vitro multistep reactions can be combined in a single step in one pot by optimizing multistep reactions under identical reaction condition. Using this analogy, the process of making PEGylated insulin, IN-105, was simplified. Instead of taking the purified active insulin bulk powder as the starting material for the conjugation step, an insulin process intermediate, partially purified insulin ester, was taken as starting material. Process intensification (PI) was established by performing a novel de-blocking (de-esterification) of the partially purified insulin ester and conjugation at B-29 Lys residue of B chain with a short-chain methoxy polyethylene glycol (mPEG) in a single-pot reactor. The chromatographic profile at the end of the reaction was found similar irrespective of whether both the reactions were performed sequentially or simultaneously. The conjugated product of interest, IN-105 (conjugation at LysB(29)), was purified from the heterogeneous mixture of conjugated products. The new manufacturing process was deduced to be more simplified and economical in making the insulin conjugates as several downstream purification steps could be circumvented. The physicochemical characteristics of IN-105 manufactured through this economic process was found to be indifferent from the product formed through the traditional process where the conjugation starting material was purified from bulk insulin.     

Bioactive extracts of Carum copticum L. enhances efficacy of ciprofloxacin against MDR enteric bacteria

The widespread occurrence of extended spectrum β-lactamases (ESβLs) producing enteric bacteria and their co-resistance with flouroquinolones has impaired the current antimicrobial therapy. This has prompted the search for new alternatives through synergistic approaches with herbal extracts. In this study Carum copticum (seeds) was extracted first in methanol and then subsequently extracted in different organic solvents. MIC of plant extracts, ciprofloxacin and thymol was determined by broth micro-dilution method using TTC. Synergism between plant extracts and ciprofloxacin was assayed by the checkerboard method. Chemical constituents of active extracts were analyzed by GC-MS. Methanolic, hexane and ether extract of Carum copticum exhibited significant antibacterial activity with MIC values ranged from 0.25 mg/ml to 2.0 mg/ml. Synergy analysis between Carum copticum extracts and ciprofloxacin combinations revealed FIC index in the range of 0.093–0.25. About 81% ciprofloxacin resistant ESβL producing enteric bacteria were re-sensitized in the presence of 15.6–250 μg/ml of methanolic extract of Carum copticum. Moreover, ciprofloxacin showed 8 to 64 folds reduction in MIC in presence of 250 and 500 μg/ml of hexane extract. Whereas, 4–32 folds reduction in MIC of ciprofloxacin was achieved in the presence of 31.25 and 62.5 μg/ml of ether extract, indicating synergistic enhancement of drug activity. The chemical analysis of hexane and ether extracts by GC-MS revealed the common occurrence of one or more phenolic hydroxyl at different locations on benzene ring. This study demonstrated the potential use of herbal extract of Carum copticum in combination therapy against ESβL producing bacteria.     

Nitrate and nitrite inhibition of methanogenesis during denitrification in granular biofilms and digested domestic sludges

Anaerobic bioreactors that can support simultaneous microbial processes of denitrification and methanogenesis are of interest to nutrient nitrogen removal. However, an important concern is the potential toxicity of nitrate (NO₃ ⁻) and nitrite (NO₂ ⁻) to methanogenesis. The methanogenic toxicity of the NO_x⁻ compounds to anaerobic granular biofilms and municipal anaerobic digested sludge with two types of substrates, acetate and hydrogen, was studied. The inhibition was the severest when the NO_x⁻ compounds were still present in the media (exposure period). During this period, 95% or greater inhibition of methanogenesis was evident at the lowest concentrations of added NO₂ ⁻ tested (7.6–10.2 mg NO₂ ⁻-N l⁻¹) or 8.3–121 mg NO₃ ⁻-N l⁻¹ of added NO₃ ⁻, depending on substrate and inoculum source. The inhibition imparted by NO₃ ⁻ was not due directly to NO₃ ⁻ itself, but instead due to reduced intermediates (e.g., NO₂ ⁻) formed during the denitrification process. The toxicity of NO_x⁻ was found to be reversible after the exposure period. The recovery of activity was nearly complete at low added NO_x⁻ concentrations; whereas the recovery was only partial at high added NO_x⁻ concentrations. The recovery is attributed to the metabolism of the NO_x⁻ compounds. The assay substrate had a large impact on the rate of NO₂ ⁻ metabolism. Hydrogen reduced NO₂ ⁻ slowly such that NO₂ ⁻ accumulated more and as a result, the toxicity was greater compared to acetate as a substrate. The final methane yield was inversely proportional to the amount of NO_x⁻ compounds added indicating that they were the preferred electron acceptors compared to methanogenesis.     

Metabolic pathways coupled to H+ transport in turtle urinary bladder

Summary Active H⁺ transport in the turtle urinary bladder is mediated by an ATPase. Although the source of ATP is usually mitochondrial oxidative phosphorylation, it is possible because of intracellular compartmentalization or cellular heterogeneity that one metabolic pathway exclusively provides ATP to the pump. To examine this we performed several types of experiments. In one, the coupling between the rate of transport and the rate of oxidation of¹⁴C-labeled substrates was studied. We found that there was coupling between H⁺ transport and glucose, butyrate, oleate, and -OH-butyrate oxidation. In another set of experiments we depleted turtle bladders of their endogenous substrates and tested the effect of a number of substrates on the rate of transport. We found that glucose, pyruvate, lactate, actetate, butyrate and -OH butyrate all stimulated H⁺ transport. In a third set of experiments we found no coupling between H⁺ transport and lactate production. Finally, we found that reduction of H⁺ transport by mucosal acidification resulted in an increase in epithelial cell ATP concentrations and a decrease in ADP levels.These results suggest that the H⁺ pump receives its ATP from carbohydrate and fatty acid oxidation. The changes in ATP and ADP levels provide an initial explanation for the coupling of H⁺ transport to the rate of cellular oxidative metabolism.     

Clinico-hormonal correlation of oligospermic patients in the below sea level environment (Jordan Valley)

A correlation between serum levels of luteinizing hormone (LH), total testosterone (T), free T and sex-hormone binding globulin (SHBG) in normospermic and in oligospermic male people was done. This study was designed to measure serum levels of these hormones and of SHBG in people living at different altitude environments relative to sea level: at 209-408 meters below (the Jordan Valley, JV) and at 620 meters above (Irbid city, IC). In addition, a clinical awareness study of oligospermia was done in the North of Jordan (IC). Seminal analysis in 287 male people (age range, 18 to 40 years old) during the period between 12/6/1999 and 12/2/2002 showed an oligospermia of 31.4%. Serum levels of LH, total T, free T and SHBG in normospermic subjects in IC were similar to those in normospermic of the JV (3.4 +/- 1.2 vs. 4.0 +/- 1.7 MIU/ml, 19.9 +/- 4.0 vs. 20.4 +/- 5.6 ng/ml, 53.9 +/- 15.6 vs. 47.9 +/- 10.7 pg/ml, 19.5 +/- 3.2 vs. 18.6 +/- 2.16 nmol/l, respectively). Oligospermia was associated with increase in total T at both IC (27.5 +/- 4.6 vs. 19.9 +/- 4.0 ng/ml) and the JV (30.7 +/- 3.4 vs. 20.5 +/- 5.6). The higher serum level of total T in oligospermic people in both IC and the JV was associated with higher levels of SHBG compared to those levels in normospermic subjects. On the other hand, oligospermic subjects have lower serum level of free T than in normospermic males (41.5 +/- 10.0 vs. 53.9 +/- 15.6) only in IC, while in the JV, serum free T level was similar (46.5 +/- 6.1 vs. 47.9 +/- 10.7). Taken together data for both locations, IC and the JV, suggest a clear correlation between total T and SHBG levels in both groups' normospermic and oligospermic subjects.