Conserving a threatened North American walnut: a chromosome-scale reference genome for butternut (Juglans cinerea)

With the advent of affordable and more accurate third-generation sequencing technologies, and the associated bioinformatic tools, it is now possible to sequence, assemble, and annotate more species of conservation concern than ever before. Juglans cinerea, commonly known as butternut or white walnut, is a member of the walnut family, native to the Eastern United States and Southeastern Canada. The species is currently listed as Endangered on the IUCN Red List due to decline from an invasive fungus known as Ophiognomonia clavigignenti-juglandacearum (Oc-j) that causes butternut canker. Oc-j creates visible sores on the trunks of the tree which essentially starves and slowly kills the tree. Natural resistance to this pathogen is rare. Conserving butternut is of utmost priority due to its critical ecosystem role and cultural significance. As part of an integrated undergraduate and graduate student training program in biodiversity and conservation genomics, the first reference genome for Juglans cinerea is described here. This chromosome-scale 539 Mb assembly was generated from over 100 × coverage of Oxford Nanopore long reads and scaffolded with the Juglans mandshurica genome. Scaffolding with a closely related species oriented and ordered the sequences in a manner more representative of the structure of the genome without altering the sequence. Comparisons with sequenced Juglandaceae revealed high levels of synteny and further supported J. cinerea's recent phylogenetic placement. Comparative assessment of gene family evolution revealed a significant number of contracting families, including several associated with biotic stress response.

An Unusual Presentation of Paroxysmal Atrial Fibrillation Following Ablation

A pheochromocytoma is a rare catecholamine-secreting tumor with an incidence of 0.8 per 100,000 person-years. Classic clinical manifestations include episodic headache, sweating, and tachycardia. This case report shares a unique presentation in which a patient with a history of atrial fibrillation status post-ablation procedure was admitted for chest pain and found to have imaging and laboratory findings consistent with pheochromocytoma. This case illustrates the importance of a high clinical index of suspicion for a pheochromocytoma since it can have a variety of clinical presentations and can result in unnecessary procedures.

Cellular molecular and proteomic profiling deciphers the SIRT1 controlled cell death pathways in esophageal adenocarcinoma cells

Worldwide prevalence of esophageal adenocarcinomas with high rates of mortality coupled with increased mutations in esophageal cells warrants investigation to understand deregulation of cell signaling pathways leading to cancer. To this end, the current study was undertaken to unravel the cell death signatures using the model human esophageal adenocarcinoma cell line-OE33. The strategy involved targeting the key epigenetic modulator SIRT1, a histone deacetylase by a small molecule inhibitor - sirtinol. Sirtinol induced a dose-dependent inhibition of cell viability under both normoxic and hypoxic conditions with long term impact on proliferation as shown by clonogenic assays. Signature apoptotic signaling pathways including caspase activation and decreased Bcl-2 were observed. Proteomic analysis highlighted an array of entities affected including molecules involved in replication, transcription, protein synthesis, cell division control, stress-related proteins, spliceosome components, protein processing and cell detoxification/degradation systems. Importantly, the stoichiometry of the fold changes of the affected proteins per se could govern the cell death phenotype by sirtinol. Sirtinol could also potentially curb resistant and recurrent tumors that reside in hypoxic environments. Overall, in addition to unraveling the cellular, molecular and proteomics basis of SIRT1 inhibition, the findings open up avenues for designing novel strategies against esophageal adenocarcinoma.

Perceptions of community nutrition and health needs in the Lower Mississippi Delta: a key informant approach

OBJECTIVE

Key informants' perceptions of nutrition and health needs in their southern rural communities were assessed prior to nutrition intervention planning.

DESIGN

This cross-sectional survey used in-person interviews.

SUBJECTS/SETTINGS

A sample of 490 individuals from 12 professional and lay roles in 8 community sectors in 36 counties in Arkansas, Louisiana, and Mississippi was chosen.

STATISTICAL ANALYSES PERFORMED

Factor analysis was carried out on reported food, nutrition, and health problems and contributing factors. The General Linear Models procedure identified within- and between-subject effects for factors. Tukey's post hoc tests identified differences between sectors and states. Frequencies and weighted rankings were computed for health problems.

RESULTS

Key informants rated individual-level factors (food choices, education, willingness to change, health behavior) as more important than community-level factors (food and health care access, resources) with regard to nutrition and health problems and contributors to problems. The number one health problem was hypertension.

IMPLICATIONS

Key informants are knowledgeable about nutrition and health problems, contributing factors, and available resources. Individual factors were perceived as more important contributors to nutrition and health problems providing valuable information for planning nutrition interventions.

Validity of a telephone-administered 24-hour dietary recall in telephone and non-telephone households in the rural Lower Mississippi Delta region

OBJECTIVE

To determine if 24-hour dietary recall data are influenced by whether data are collected by telephone or face-to-face interviews in telephone and non-telephone households.

DESIGN

Dual sampling frame of telephone and non-telephone households. In telephone households, participants completed a 24-hour dietary recall either by face-to-face interview or telephone interview. In non-telephone households, participants completed a 24-hour dietary recall either by face-to-face interview or by using a cellular telephone provided by a field interviewer.

SUBJECTS/SETTING

Four hundred nine participants from the rural Delta region of Arkansas, Louisiana, and Mississippi.

MAIN OUTCOME MEASURES

Mean energy and protein intakes.

STATISTICAL ANALYSES PERFORMED

Comparison of telephone and non-telephone households, controlling for type of interview, and comparison of telephone and face-to-face interviews in each household type using unpaired t tests and linear regression, adjusting for gender, age, and body mass index.

RESULTS

Mean differences between telephone and face-to-face interviews for telephone households were -171 kcal (P = 0.1) and -6.9 g protein (P = 0.2), and for non-telephone households -143 kcal (P = 0.6) and 0.4 g protein (P = 1.0). Mean differences between telephone and non-telephone households for telephone interviews were 0 kcal (P = 1.0) and -0.9 g protein (P = 0.9), and for face-to-face interviews 28 kcal (P = 0.9) and 6.4 g protein (P = 0.5). Findings persisted when adjusted for gender, age, and body mass index. No statistically significant differences were detected for mean energy or protein intake between telephone and face-to-face interviews or between telephone and non-telephone households.

APPLICATIONS/CONCLUSIONS

These data provide support that telephone surveys adequately describe energy and protein intakes for a rural, low-income population.

Recognition of misfolding proteins by PA700, the regulatory subcomplex of the 26 S proteasome

The 26 S proteasome is a large protease complex that catalyzes the degradation of both native and misfolded proteins. These proteins are known to interact with PA700, the regulatory subcomplex of the 26 S proteasome, via a covalently attached polyubiquitin chain. Here we provide evidence for an additional ubiquitin-independent mode of substrate recognition by PA700. PA700 prevents the aggregation of three incompletely folded, nonubiquitinated substrates: the DeltaF-508 mutant form of cystic fibrosis transmembrane regulator, nucleotide binding domain 1, insulin B chain, and citrate synthase. This function does not require ATP hydrolysis. The stoichiometry required for this function, the effect of PA700 on the lag phase of aggregation, and the temporal specificity of PA700 in this process all indicate that PA700 interacts with a subpopulation of non-native conformations that is either particularly aggregation-prone or nucleates misassociation reactions. The inhibition of off-pathway self-association reactions is also reflected in the ability of PA700 to promote refolding of citrate synthase. These results provide evidence that, in addition to binding polyubiquitin chains, PA700 contains a site(s) that recognizes and interacts with misfolded or partially denatured polypeptides. This feature supplies an additional level of substrate specificity to the 26 S proteasome and a means by which substrates are maintained in a soluble state until refolding or degradation is complete.

Cystic fibrosis transmembrane conductance regulator regulates luminal Cl-/HCO3- exchange in mouse submandibular and pancreatic ducts

We have demonstrated previously the regulation of Cl-/HCO3- exchange activity by the cystic fibrosis transmembrane conductance regulator (CFTR) in model systems of cells stably or transiently transfected with CFTR (Lee, M. G., Wigley, W. C., Zeng, W., Noel, L. E., Marino, C. R., Thomas, P. J., and Muallem, S. (1999) J. Biol. Chem. 274, 3414-3421). In the present work we examine the significance of this regulation in cells naturally expressing CFTR. These include the human colonic T84 cell line and the mouse submandibular gland and pancreatic ducts, tissues that express high levels of CFTR in the luminal membrane. As in heterologous expression systems, stimulation of T84 cells with forskolin increased the Cl-/HCO3- exchange activity independently of CFTR Cl- channel activity. Freshly isolated submandibular gland ducts from wild type mice showed variable Cl-/HCO3- exchange activity. Measurement of [Cl-]i revealed that this was largely the result of variable steady-state [Cl-]i. Membrane depolarization with 5 mM Ba2+ or 100 mM K+ increased and stabilized [Cl-]i. Under depolarized conditions wild type and DeltaF/DeltaF mice had comparable basal Cl-/HCO3- exchange activity. Notably, stimulation with forskolin increased Cl-/HCO3- exchange activity in submandibular gland ducts from wild type but not DeltaF/DeltaF mice. Microperfusion of the main pancreatic duct showed Cl-/HCO3- exchange activity in both the basolateral and luminal membranes. Stimulation of ducts from wild type animals with forskolin had no effect on basolateral but markedly stimulated luminal Cl-/HCO3- exchange activity. By contrast, forskolin had no effect on either basolateral or luminal Cl-/HCO3- exchange activity of ducts from DeltaF/DeltaF animals. We conclude that CFTR regulates luminal Cl-/HCO3- exchange activity in CFTR-expressing cells, and we discuss the possible physiological significance of these findings regarding cystic fibrosis.

The molecular chaperone Hsc70 assists the in vitro folding of the N-terminal nucleotide-binding domain of the cystic fibrosis transmembrane conductance regulator

The most common disease-causing mutation in the cystic fibrosis transmembrane conductance regulator is a single amino acid deletion (DeltaF508) in the N-terminal cytosolic nucleotide-binding domain (NBD1). This mutation has previously been shown to be a temperature-sensitive folding mutation that alters the folding pathway but not the native state stability of the isolated domain (Qu, B.-H., and Thomas, P. J. (1996) J. Biol. Chem. 271, 7261-7264). Here we provide evidence that the molecular chaperone Hsc70 productively interacts with NBD1 to increase the folding yield of the domain and inhibit off-pathway associations leading to the formation of high molecular weight aggregates. Furthermore, we have sublocalized a region within NBD1 where Hsc70 binds. Notably, inhibition of NBD1 aggregation is not dependent upon the presence of Hsc70 in the early stages of folding, indicating that the chaperone may act on a folding intermediate. In the presence of K+ and Mg2+-ATP, conditions where Hsp70 binds substrate rapidly and can release it, Hsc70 is less effective at inhibiting NBD1 aggregation. Thus, the rate of release of unfolded substrate is an important factor in preventing aggregation and promoting folding of the domain. These results demonstrate that Hsc70 promotes the otherwise inefficient folding of DeltaF-NBD1 and provide insight into the mechanisms by which molecular chaperones assist proteins in folding.

Cystic fibrosis: a disease of altered protein folding

Cystic fibrosis (CF) is caused by mutations in the gene that encodes the cystic fibrosis transmembrane conductance regulator, CFTR. Previously we demonstrated that the common delta F508 mutation in the first nucleotide binding domain (NBD1) alters the ability of the domain to fold into a functional three-dimensional structure, providing a molecular explanation for the observation that the mutant CFTR is retained in the endoplasmic reticulum and does not traffic to the apical membrane of affected epithelial cells. Notably, when conditions are altered to promote folding of the mutant protein, it can assume a functional conformation. Correcting the folding defect may have therapeutic benefit for the treatment of cystic fibrosis. Here we summarize these results and discuss the implications in vitro folding studies have for understanding the pathobiology of CF.

Strategy for recombinant multichain protein synthesis: fibrinogen B beta-chain variants as thrombin substrates

Thrombotic disease has been found in patients with congenital dysfibrinogens that have abnormalities in the amino terminal domain of the fibrinogen B beta-chain. Surprisingly, these fibrinogens are poor substrates for thrombin. In order to examine the molecular basis for this impaired thrombin-fibrinogen interaction, we synthesized three fibrinogens with single amino acid substitutions in this domain: B beta A68T, B beta P70S, and B beta L72S. B beta-chain expression vectors were altered by PCR-directed mutagenesis of the B beta cDNA. The altered vectors were transfected into a Chinese hamster ovary (CHO) cell line that was constructed as a first step in recombinant fibrinogen synthesis, this CHO line synthesizes fibrinogen A alpha- and gamma-chains. More than 86% of the stably selected clones expressed significant levels of fibrinogen, confirming that a two-step strategy permitted efficient synthesis of variant fibrinogens. In large-scale cultures variant fibrinogen accumulation in serum-free medium fluctuated between 1 and 15 micrograms/mL. Normal and variant recombinant fibrinogens were compared to plasma fibrinogens by following the time course of thrombin-catalyzed release of fibrinopeptides. Only the variant B beta A68T, a change identified in a congenital dysfibrinogen, showed significantly impaired kinetics. The rate of fibrinopeptide A release was decreased 27-fold, and the rate of fibrinopeptide B release was decreased 45-fold relative to normal fibrinogen. Fibrinopeptide release was not significantly altered by the substitutions B beta P70S or B beta L72S. These results suggest that B beta residue Ala68 has a novel and critical role in the interaction between thrombin and fibrinogen.

Purification and characterization of recombinant human fibrinogen

Our laboratory has been using protein engineering to study the relationship of primary structure to fibrinogen function. In order to examine genetically altered domains in the context of the intact, functional fibrinogen molecule, we have expressed recombinant human fibrinogen in Chinese Hamster Ovary (CHO) cells. The cDNA for each fibrinogen chain was individually cloned into the same expression vector. Each vector was cotransfected with the selection vector pRSVneo into CHO cells. In addition, the plasmids encoding A alpha and gamma were cotransfected with pRSVneo. Cells resistant to G418, a neomycin analogue, were isolated and clonal lines developed. Analysis of these lines demonstrated that CHO cells express and secrete free gamma chain, and an A alpha-gamma complex. To obtain recombinant fibrinogen, the A alpha-gamma G418-resistant clones were transfected with the B beta expression plasmid and a second selection vector, pMSVhis. Colonies resistant to neomycin and histidinol were selected and clonal lines obtained. These clones secreted biologically active recombinant human fibrinogen, which was purified from serum-free culture media by protamine-Sepharose chromatography. Analysis of the purified protein on SDS-polyacrylamide gels demonstrated a pattern indistinguishable from plasma fibrinogen. Removal of Asn-linked carbohydrate with glycosidase F revealed the presence of carbohydrate on the B beta and gamma chains, as is seen for plasma fibrinogen.

Characterization of purified recombinant fibrinogen: partial phosphorylation of fibrinopeptide A

Human fibrinogen has been expressed in Chinese hamster ovary (CHO) cells using a novel two-step procedure which permits efficient synthesis of engineered variant fibrinogens. CHO cells secreting recombinant fibrinogen were grown in roller bottles and maintained in serum-free media for several months. Recombinant protein was purified from media containing 2-4 micrograms/mL fibrinogen using protamine-Sepharose chromatography. Recombinant fibrinogen was identical to plasma fibrinogen when examined on Coomassie-stained SDS gels run under reducing conditions, and on SDS gels when run under nonreducing conditions after partial or complete plasmin degradation, indicating normal chain assembly, disulfide bond formation, and overall protein conformation. Thrombin digestion of purified fibrinogen led to clot formation with release of normal fibrinopeptides, as identified by HPLC. Fibrinopeptide A released from recombinant fibrinogen was partially phosphorylated (22%), similar to the degree of phosphorylation found for human plasma fibrinogen (20-25%), indicating that partial phosphorylation in inherent in fibrinogen synthesis.

The effect of oxidase positive bacteria on total coliform density estimates

The most probable number method for enumerating coliforms was shown to give a false estimate of the coliform density. The inflated estimates were due to lactose positive, non-coliform bacteria whose presence was detected by an oxidase test. Thirty-six percent of all the samples examined contained oxidase positive bacteria that were able to produce gas from lactose. Their presence resulted in coliform density overestimates which ranged from 2 to 33 times the true value. The frequency of occurrence of inaccurate estimates was shown to be affected by water temperature but unrelated to environmental source.