Ovarian development, spawning frequency and batch fecundity in Encrasicholina heteroloba (Ruppell, 1858)

A histological and gravimetric analysis of oocyte development in Encrasicholina heteroloba (Ruppell, 1858) indicated that this species spawns serially and has a group-synchronous mode of ovarian development. A six stage maturity scale, based on both external morphology and oocyte composition, was proposed to classify ovarian development in E. heteroloba . The incidence of females with hydrated oocytes and post-ovulatory follicles in samples from two regions; the south Java Sea and Roviana lagoon, in the Solomon Islands were used to estimate spawning frequency. Estimates of mean inter-spawning intervals ranged from around 2 days in fish from Roviana lagoon to up to 16.7 days in fish from the south Java Sea. Batch fecundity was determined from the number of oocytes in the largest oocyte size class in ripe stage ovaries. Batch fecundity was related to size and was significantly greater for a given size in the Roviana lagoon population ( F = 0.081 × L ^4.89, Roviana population; F = 1.682 × L ^2.83, Jepara population).     

Nucleotide-Dependent Isomerization of Glutamate Dehydrogenase in Relation to Total RNA Contents of Peanut

The physiological function of glutamate dehydrogenase (GDH) was investigated by treating germinating peanut (Arachis hypogaea L.) seeds with nucleoside triphosphate (NTP) solutions in order to alter the isoenzyme distribution patterns. The free nucleosides and nucleotides of the GTP-treated peanut were the highest [8.7 μmol g⁻¹(f.m.)], and they decreased through the ATP-treated peanut [5.8 μmol g⁻¹(f.m.)], and CTP-treated peanut [5.5 μmol g⁻¹(f.m.)], to the UTP-treated peanut [4.1 μmol g⁻¹(f.m.)]. The combination of 4 NTPs induced 20 % higher content of Pi [173 nmol g⁻¹(f.m.)] than in the control, but the combined ATP+UTP treatment induced the lowest (93.0 nmol g⁻¹(f.m.)] Pi. The 4 NTP treatment also induced the highest number of GDH isoenzymes (28) followed by the purine NTP treatments (15 to 20), but the pyrimidine NTP treatments and the combined purine + pyrimidine NTP treatments induced the lowest numbers (<15) of isoenzymes. The deamination/amination ratios were generally higher in the UTP (0.11), and CTP (0.06) treated peanuts than in the GTP (0.04), and ATP (0.07) treated peanuts. There were mutual relationships between higher numbers of GDH isoenzymes present in the GTP-, and ATP-treated peanuts and higher RNA (236.5 and 239.4 μg g⁻¹, respectively) contents on one hand, and between the lower numbers of isoenzymes in the CTP-, and UTP-treated peanuts and lower RNA (162.0 and 152.5 μg g⁻¹, respectively) contents. The recurrent relationships of the effects of the NTP treatments of peanut were UTP > ATP > CTP > GTP. This revised version was published online in July 2006 with corrections to the Cover Date.     

Influence of phosphate rock sources and rates on rice and common bean production in an Oxisol

A field experiment was conducted for five consecutive years to determine upland rice (Oryza sativa L.) and common bean (Phaseolus vulgaris L.) response to eight P sources at three P rates in an Oxisol of Central Brazil. The P sources tested were triple superphosphate (TSP), Arafertil phosphate partially acidulated (APPA), phosphate of Patos partially acidulated (PPPA), phosphate of Araxa concentrated (PAC), phosphate of Catalao (PC), phosphate of Jacupiranga (PJ), phosphate of Patos de Minas (PPM), and phosphate of Abaete (PA). All phosphate rock sources were of Brazilian origin. The P rates used were 87, 174 and 262 kg P ha^-1. Yield response to P sources and rates varied from crop to crop. Rice and bean yields were significantly correlated with Bray 1 P, but not Mehlich 1 P. In the first year, TSP and the two partially acidulated phosphate rocks (APPA, PPPA) produced higher grain yields. In the second year and all remaining years of the experiment, the efficiency of phosphate rock sources as measured by grain yield was equivalent to TSP or partially acidulated P sources. The results suggest that these phosphate rock sources could be used in rice-bean rotations on Brazilian Oxisols. Yield losses in the first year could be partially offset by the addition of a small amount of soluble P.     

Systematic Screening of Drosophila Deficiency Mutations for Embryonic Phenotypes and Orphan Receptor Ligands

This paper defines a collection of Drosophila deletion mutations (deficiencies) that can be systematically screened for embryonic phenotypes, orphan receptor ligands, and genes affecting protein localization. It reports the results of deficiency screens we have conducted that have revealed new axon guidance phenotypes in the central nervous system and neuromuscular system and permitted a quantitative assessment of the number of potential genes involved in regulating guidance of specific motor axon branches. Deficiency “kits” that cover the genome with a minimum number of lines have been established to facilitate gene mapping. These kits cannot be systematically analyzed for phenotypes, however, since embryos homozygous for many deficiencies in these kits fail to develop due to the loss of key gene products encoded within the deficiency. To create new kits that can be screened for phenotype, we have examined the development of the nervous system in embryos homozygous for more than 700 distinct deficiency mutations. A kit of ∼400 deficiency lines for which homozygotes have a recognizable nervous system and intact body walls encompasses >80% of the genome. Here we show examples of screens of this kit for orphan receptor ligands and neuronal antigen expression. It can also be used to find genes involved in expression, patterning, and subcellular localization of any protein that can be visualized by antibody staining. A subset kit of 233 deficiency lines, for which homozygotes develop relatively normally to late stage 16, covers ∼50% of the genome. We have screened it for axon guidance phenotypes, and we present examples of new phenotypes we have identified. The subset kit can be used to screen for phenotypes affecting all embryonic organs. In the future, these deficiency kits will allow Drosophila researchers to rapidly and efficiently execute genome-wide anatomical screens that require examination of individual embryos at high magnification.     

Identifiability in biobanks: models,measures, and mitigation strategies

The collection and sharing of person-specific biospecimens has raised significant questions regarding privacy. In particular, the question of identifiability, or the degree to which materials stored in biobanks can be linked to the name of the individuals from which they were derived, is under scrutiny. The goal of this paper is to review the extent to which biospecimens and affiliated data can be designated as identifiable. To achieve this goal, we summarize recent research in identifiability assessment for DNA sequence data, as well as associated demographic and clinical data, shared via biobanks. We demonstrate the variability of the degree of risk, the factors that contribute to this variation, and potential ways to mitigate and manage such risk. Finally, we discuss the policy implications of these findings, particularly as they pertain to biobank security and access policies. We situate our review in the context of real data sharing scenarios and biorepositories.     

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

Bacterioplankton of the SAR11 clade are the most abundant microorganisms in marine systems, usually representing 25% or more of the total bacterial cells in seawater worldwide. SAR11 is divided into subclades with distinct spatiotemporal distributions (ecotypes), some of which appear to be specific to deep water. Here we examine the genomic basis for deep ocean distribution of one SAR11 bathytype (depth-specific ecotype), subclade Ic. Four single-cell Ic genomes, with estimated completeness of 55%–86%, were isolated from 770 m at station ALOHA and compared with eight SAR11 surface genomes and metagenomic datasets. Subclade Ic genomes dominated metagenomic fragment recruitment below the euphotic zone. They had similar COG distributions, high local synteny and shared a large number (69%) of orthologous clusters with SAR11 surface genomes, yet were distinct at the 16S rRNA gene and amino-acid level, and formed a separate, monophyletic group in phylogenetic trees. Subclade Ic genomes were enriched in genes associated with membrane/cell wall/envelope biosynthesis and showed evidence of unique phage defenses. The majority of subclade Ic-specfic genes were hypothetical, and some were highly abundant in deep ocean metagenomic data, potentially masking mechanisms for niche differentiation. However, the evidence suggests these organisms have a similar metabolism to their surface counterparts, and that subclade Ic adaptations to the deep ocean do not involve large variations in gene content, but rather more subtle differences previously observed deep ocean genomic data, like preferential amino-acid substitutions, larger coding regions among SAR11 clade orthologs, larger intergenic regions and larger estimated average genome size.     

The strength-dexterity test as a measure of dynamic pinch performance

We have developed a method to quantify the dynamic interaction between fingertip force magnitude (strength) and directional control (dexterity) during pinch with a novel strength-dexterity (S-D) test based on the principle of buckling of compression springs. The test consists of asking participants to use key and opposition pinch to attempt to fully compress springs, in random order, with a wide range of combinations of strength and dexterity requirements. The minimum force required to fully compress the spring and the propensity of the spring to buckle define the strength and dexterity requirements, respectively. The S-D score for each pinch style was the sum of the strength values of all springs successfully compressed fully. We tested 3 participant groups: 18 unimpaired young adults (40yr), and 14 adults diagnosed with carpo-metacarpal osteoarthritis (CMC OA) (>or = 36yr). We investigated the repeatability of the S-D test with 74 springs by testing 14 young adults twice on different days. The per-spring repeatability across subjects was >or = 94%. A minimum performance score for young adults was found as they all could compress a subset of 39 springs. Using this subset of springs, we compared the ability of the S-D score vs. maximal pinch force values to distinguish unimpaired hands from those with CMC OA of the thumb. The score for this 39-spring S-D test distinguished between CMC OA and asymptomatic older adults, whereas pinch meter readings did not (p<0.05). We conclude that the S-D test is repeatable and applicable to clinical research. We propose including the S-D test in studies aiming to quantify impairment and compare treatment outcomes in orthopaedic and neurological afflictions that degrade dynamic manipulation.     

Polyarginines are potent furin inhibitors

The ubiquitous serine endoprotease furin has been implicated in the activation of bacterial toxins and viral glycoproteins as well as in the metastatic progression of certain tumors. Although high molecular mass bioengineered serpin inhibitors have been well characterized, no small nontoxic nanomolar inhibitors have been reported to date. Here we describe the identification of such inhibitors using positional scanning amidated and acetylated synthetic l- and d-hexapeptide combinatorial libraries. The results indicated that l-Arg or l-Lys in all positions generated the most potent inhibitors. However, further investigation revealed that the peptide terminating groups hindered inhibition. Consequently, a series of non-amidated and acetylated polyarginines was synthesized. The most potent inhibitor identified, nona-l-arginine, had a K(i) for furin of 40 nm. The K(i) values for the related convertases PACE4 and prohormone convertase-1 (PC1) were 110 nm and 2.5 microm, respectively. Although nona-l-arginine was cleaved by furin, the major products after a 6-h incubation at 37 degrees C were hexa- and hepta-l-arginines, both of which retained the great majority of their potency and specificity against furin. Hexa-d-arginine was as potent and specific a furin inhibitor as hexa-l-arginine (K(i) values of hexa-d-arginine: 106 nm, 580 nm, and 13.2 microm for furin, PACE4, and PC1, respectively). PC2 was not inhibited by any polyarginine tested; indeed, PC2 showed an increase in activity of up to 140% of the control in the presence of l-polyarginines. Data are also presented that show extended subsite recognition by furin and PC2. Whereas N-terminal acetylation was found to reduce the inhibitory potency of the l-hexapeptide LLRVKR against furin 8-fold, C-terminal amidation reduced the potency < 2-fold. Conversely, N-terminal acetylation increased the potency against PC2 nearly 3-fold, whereas C-terminal amidation of the same peptide increased the potency by a factor of 1.6. Our data indicate that non-acetylated, poly-d-arginine-derived molecules may represent excellent lead compounds for the development of therapeutically useful furin inhibitors.