scholarly journals Recovering Population Parameters from a Single Gene Genealogy: An Unbiased Estimator of the Growth Rate

2010 ◽  
Vol 28 (5) ◽  
pp. 1617-1631 ◽  
Author(s):  
Yosef E. Maruvka ◽  
Nadav M. Shnerb ◽  
Yaneer Bar-Yam ◽  
John Wakeley
Keyword(s):  
Growth Rate ◽  
Unbiased Estimator ◽  
Single Gene ◽  
Population Parameters ◽  
Gene Genealogy

scholarly journals CRISPR-Cas9 mutagenesis and single gene reintegration suggests functional diversity within the Candida albicans TLO gene family

2021 ◽  
Vol 3 (12) ◽  
Author(s):  
Jessica Fletcher ◽  
Gary Moran ◽  
Derek Sullivan
Keyword(s):  
Growth Rate ◽  
Candida Albicans ◽  
Gene Family ◽  
Biofilm Formation ◽  
Single Gene ◽  
Hyphal Growth ◽  
Detectable Effect ◽  
Null Mutant ◽  
Phenotypic Analysis ◽  
Functional Differences

Candida albicans has between 10-15 Telomere-associated ORF family(TLO)genes, whereas its closest relative, Candida dubliniensis, has two. The Tlo proteins are components of the Mediator complex which plays an important role in transcriptional regulation. CRISPR-Cas9 mutagenesis was used to generate a TLOnull mutant of C. albicans. Phenotypic analysis of the mutant showed significantly reduced fitness, with major defects in growth rate, morphogenesis, stress resistance and virulence in a Galleria mellonellamodel. Clade representative TLOα1, TLOβ2 and TLOγ11constructs were reintroduced into the null mutant background to determine if members of the TLO gene family exhibit functional differences. The genes were reintroduced under the control of the TET1 and ENO1promoters. TLOα1and TLOβ2expression restored stress tolerance and growth rate, in some cases to the level of the WT. TLOβ2expression also showed a dramatic effect on morphology resulting in constitutive true hyphal growth. Moderate expression of TLOγ11 had no detectable effect on many of the phenotypes tested, however overexpression increased biofilm formation in Spider medium, and also conferred increased resistance to cell wall stressors. These data suggest that individual TLO genes have distinct functions and that the diversity within the TLO family may contribute to the relative success of C. albicans as a coloniser and pathogen of humans.

scholarly journals Metabolome Analysis of Constituents in Membrane Vesicles for Clostridium thermocellum Growth Stimulation

2021 ◽  
Vol 9 (3) ◽  
pp. 593
Author(s):  
Shunsuke Ichikawa ◽  
Yoichiro Tsuge ◽  
Shuichi Karita
Keyword(s):  
Growth Rate ◽  
Clostridium Thermocellum ◽  
Consolidated Bioprocessing ◽  
Membrane Vesicle ◽  
Single Gene ◽  
Membrane Vesicles ◽  
Growth Stimulation ◽  
Cellulosic Biomass ◽  
Cellulolytic Bacterium ◽  
Metabolome Analysis

The cultivation of the cellulolytic bacterium, Clostridium thermocellum, can have cost-effective cellulosic biomass utilizations, such as consolidated bioprocessing, simultaneous biological enzyme production and saccharification. However, these processes require a longer cultivation term of approximately 1 week. We demonstrate that constituents of the C. thermocellum membrane vesicle fraction significantly promoted the growth rate of C. thermocellum. Similarly, cell-free Bacillus subtilis broth was able to increase C. thermocellum growth rate, while several B. subtilis single-gene deletion mutants, e.g., yxeJ, yxeH, ahpC, yxdK, iolF, decreased the growth stimulation ability. Metabolome analysis revealed signal compounds for cell–cell communication in the C. thermocellum membrane vesicle fraction (ethyl 2-decenoate, ethyl 4-decenoate, and 2-dodecenoic acid) and B. subtilis broth (nicotinamide, indole-3-carboxaldehyde, urocanic acid, nopaline, and 6-paradol). These findings suggest that the constituents in membrane vesicles from C. thermocellum and B. subtilis could promote C. thermocellum growth, leading to improved efficiency of cellulosic biomass utilization.

scholarly journals TRUKTUR UKURAN DAN BEBERAPA PARAMETER POPULASI IKAN CAKALANG (Katsuwonus pelamis Linnaeus, 1758) DI SAMUDERA PASIFIK UTARA PAPUA

2017 ◽  
Vol 9 (2) ◽  
pp. 113
Author(s):  
Thomas Hidayat ◽  
Tegoeh Noegroho ◽  
Karsono Wagiyo
Keyword(s):  
Growth Rate ◽  
Mortality Rate ◽  
Size Structure ◽  
Fork Length ◽  
Total Mortality ◽  
Status Quo ◽  
Skipjack Tuna ◽  
Population Parameters ◽  
Katsuwonus Pelamis ◽  
Exploitation Rate

Ikan cakalang (Katsuwonus pelamis Linnaeus, 1758) merupakan salah satu sumberdaya ikan pelagis besar yang mempunyai nilai ekonomis penting. Informasi mengenai struktur ukuran dan beberapa parameter populasinya masih sangat terbatas khususnya di perairan Indonesia timur. Penelitian ini dilakukan di Morotai, Biak dan Jayapura dari Januari sampai Desember 2013. Tujuan penelitian ini adalah untuk menganalisis ukuran ikan yang tertangkap dan menganalisis parameter populasi meliputi laju pertumbuhan, mortalitas dan tingkat eksploitasi. Estimasi parameter pertumbuhan, mortalitas dan laju eksploitasi dihitung menggunakan program FiSAT (FAO-ICLARM Stock Assessement Tools). Ukuran ikan cakalang hasil tangkapan pancing tonda dan pancing ulur berkisar antara 15 – 94 cmFL (Fork Length), dengan modus antara 40-45 cmFL. Ukuran pertama kali tertangkap sebesar 40,1 cmFL dan kebanyakan adalah ukuran ikan yang sedang memijah. Hasil analisis menggunakan FiSAT II diperoleh laju pertumbuhan (K) sebesar 0,41/tahun, panjang asimptotik (L) 101,85 cmFL. Laju kematian alami (M) 0,6 / tahun, laju kematian karena penangkapan (F) 0,62 /tahun dan laju mortalitas total (Z) 1,22 /tahun. Tingkat eksploitasi ikan cakalang hampir fully exploited (E= 0,46). Disarankan tidak perlu ada penambahan upaya penangkapan atau status quo untuk menjaga agar sumberdaya ikan cakalang tetap terjaga kelestariannya. Skipjack tuna (Katsuwonus pelamis Linnaeus, 1758) is one of the large pelagic fish resources which have high economic value. Information on the size structure and population parameters is still limited especially in the waters of eastern Indonesia. The Research was conducted from January to December 2013 at Morotai, Biak and Jayapura. The aim of this study was to analyze the size of the fish caught and some of population parameters such as the growth rate, mortality rates, and exploitation rate. Estimated of growth parameters, mortality and exploitation rate using the program FiSAT (FAO-ICLARM Stock Assessement Tools). The size of skipjack tuna caught by troll line and handline in between 15-94 cmFL, with a mode of 40-45 cmFL. The Length at first capture was 40.1 cmFL, most of them had condition of spawning. By using program FiSAT II analysis resulted that growth rate (K) of skipjack tuna was 0.41/year, with length asimptotik (L) reaches 101.85 cmFL. The natural mortality rate (M) was 0.6 / year. The fishing mortality rate (F) was 0.62 / year and total mortality rate (Z) was 1.22 / year. The exploitation rate of skipjack tuna was nearly fully exploited (E = 0.46). It was recommended the exploitation rate of this fish should be no additional effort (status quo) to keep sustainability of the skipjack tuna resource.

scholarly journals Population structure of the bivalve Anomalocardia brasiliana, (Gmelin, 1791) in the semi-arid estuarine region of northeastern Brazil

2013 ◽  
Vol 73 (4) ◽  
pp. 819-833 ◽  
Author(s):  
AML Rodrigues ◽  
CM Borges-Azevedo ◽  
RS Costa ◽  
GG Henry-Silva
Keyword(s):  
Growth Rate ◽  
Population Structure ◽  
Sampling Site ◽  
Northeastern Brazil ◽  
Population Parameters ◽  
Intertidal Area ◽  
Semi Arid Region ◽  
Estuarine Region ◽  
Semi Arid ◽  
Heavy Rains

For several decades, the bivalve mollusk Anomalocardia brasiliana has been extracted in estuarine areas in the semi-arid region of northeastern Brazil. However, information on both dynamics and abundance of their populations are missing. In this context, the present study, therefore, investigated several aspects of the population structure of A. brasiliana on beaches near the estuary of the Apodi River in Northeast Brazil. The aims were to determine the population density of A. brasiliana during different times of the year, to estimate population parameters, and to relate species density and distribution to the abiotic characteristics of the region. Sampling was performed from March/2007 and May/2008, we collected samples of sediments and mollusks along 180 m transects in the intertidal area on the beaches Barra and Pernambuquinho, Grossos - RN. At each sampling site, samples of sediments and mollusks were collected in the intertidal area along 180 m transects. The highest and lowest average densities on Pernambuquinho beach were 1148 (April/2007), and 100 individuals.m–2 (May/ 2008), respectively. On Barra beach, the highest and lowest densities were 1813 (April/2007) and 951 individuals.m–2, (November/2007), respectively. The densities of A. brasiliana on both beaches were significantly different only in the months of January, April and May/ 2008. Length of the individuals ranged from 1 to 28 mm, with most individuals measuring between 22 and 24 mm. Length growth rate parameters for A. brasiliana were L∞ = 28.68 mm and k = 0.61 year–1 on Barra beach, and L∞ = 29.87 mm and k = 0.48 year–1 on Pernambuquinho beach. The growth rate curves for A. brasiliana suggest the presence of three well defined cohorts, thus pointing to a continuous reproduction cycle with peak recruitment between October/2007 and March/2008. A. brasiliana density decreased predominantly during the heavy rains of 2008, probably due to an accumulation of sediments and decreasing salinity. This disturbance probably affected population of this species in the region.

scholarly journals Coccidioides posadasii Contains a Single 1,3-β-Glucan Synthase Gene That Appears To Be Essential for Growth

2005 ◽  
Vol 4 (1) ◽  
pp. 111-120 ◽  
Author(s):  
Ellen M. Kellner ◽  
Kris I. Orsborn ◽  
Erin M. Siegel ◽  
M. Alejandra Mandel ◽  
Marc J. Orbach ◽  
...  
Keyword(s):  
Growth Rate ◽  
Cell Wall ◽  
Microscopic Examination ◽  
Null Allele ◽  
Single Gene ◽  
Protein Product ◽  
Wild Type ◽  
Coccidioides Posadasii ◽  
Glucan Synthase ◽  
High Degree

ABSTRACT 1,3-β-Glucan synthase is responsible for the synthesis of β-glucan, an essential cell wall structural component in most fungi. We sought to determine whether Coccidioides posadasii possesses genes homologous to known fungal FKS genes that encode the catalytic subunit of 1,3-β-glucan synthase. A single gene, designated FKS1, was identified, and examination of its predicted protein product showed a high degree of conservation with Fks proteins from other filamentous fungi. FKS1 is expressed at similar levels in mycelia and early spherulating cultures, and expression decreases as the spherules mature. We used Agrobacterium-mediated transformation to create strains that harbor ΔFKS1::hygB, a null allele of FKS1, and hypothesize that Fks1p function is essential, due to our inability to purify this allele away from a complementing wild-type FKS1 allele in a heterokaryotic strain. The heterokaryon appears normal with respect to growth rate and arthroconidium production; however, microscopic examination of strains with ΔFKS1::hygB alleles revealed abnormal swelling of hyphal elements.

Ageing studies on three species of freshwater mussels from a metal-polluted watershed in Nova Scotia, Canada

1992 ◽  
Vol 70 (7) ◽  
pp. 1284-1291 ◽  
Author(s):  
Janice L. Metcalfe-Smith ◽  
Roger H. Green
Keyword(s):  
Growth Rate ◽  
Nova Scotia ◽  
Shell Length ◽  
Metal Pollution ◽  
Freshwater Mussels ◽  
Population Parameters ◽  
Elliptio Complanata ◽  
Growth Bands ◽  
Mussel Shells ◽  
Age Estimates

Freshwater mussels are increasingly used to monitor metal pollution in freshwater systems. Mussels are long-lived, and age is a factor that may influence metal concentrations in their tissues. Species that can be precisely aged are most suitable for biomonitoring because they can be standardized for this factor. Precise age estimates are also needed for determining the effects of contamination on population parameters such as growth rate. Elliptio complanata, Anodonta implicata, and Alasmidonta undulata (family Unionidae) were collected from two Nova Scotia lakes contaminated with arsenic and mercury. Mussel shells were weighed, measured, and sectioned, and two independent counts of internal growth bands were made. External rings were also counted for A. implicata. Age estimates based on internal bands were most precise for E. complanata (r2 = 0.71 vs. 0.35 for A. implicata and 0.29 for A. undulata). Estimates based on external rings were more precise (r2 = 0.69) than those based on internal bands for A. implicata, but were believed to include disturbance rings. Shell length and weight were similarly correlated with age for a given species and population, but relationships were less clear in the lake with the more variable habitat. Elliptio complanata were much smaller at a given age in the more contaminated lake.

scholarly journals Genome-wide phenotypic analysis of growth, cell morphogenesis and cell cycle events in Escherichia coli.

2017 ◽  
Author(s):  
Manuel Campos ◽  
Sander K Govers ◽  
Irnov Irnov ◽  
Genevieve S Dobihal ◽  
Francois Cornet ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Cell Cycle ◽  
Growth Rate ◽  
Cell Division ◽  
Cell Size ◽  
Gene Knockout ◽  
Single Gene ◽  
Cell Morphogenesis ◽  
Phenotypic Analysis ◽  
New Genes

Cell size, cell growth and the cell cycle are necessarily intertwined to achieve robust bacterial replication. Yet, a comprehensive and integrated view of these fundamental processes is lacking. Here, we describe an image-based quantitative screen of the single-gene knockout collection of Escherichia coli, and identify many new genes involved in cell morphogenesis, population growth, nucleoid (bulk chromosome) dynamics and cell division. Functional analyses, together with high-dimensional classification, unveil new associations of morphological and cell cycle phenotypes with specific functions and pathways. Additionally, correlation analysis across ~4,000 genetic perturbations shows that growth rate is surprisingly not predictive of cell size. Growth rate was also uncorrelated with the relative timings of nucleoid separation and cell constriction. Rather, our analysis identifies scaling relationships between cell size and nucleoid size and between nucleoid size and the relative timings of nucleoid separation and cell division. These connections suggest that the nucleoid links cell morphogenesis to the cell cycle.

scholarly journals Population parameters as a way to evaluate the risk of attack of Aphis craccivora (Hemiptera: Aphididae) on cowpea

2020 ◽  
Vol 87 ◽  
Author(s):  
Antonia Débora Camila de Lima Ferreira ◽  
Leandro Carvalho da Silva ◽  
Daniel Rodrigues Nere ◽  
Ervino Bleicher
Keyword(s):  
Growth Rate ◽  
Population Based ◽  
Life Tables ◽  
Aphis Craccivora ◽  
Population Parameters ◽  
Adult Females ◽  
Finite Growth ◽  
Aphis Craccivora Koch ◽  
Susceptible Control ◽  
Risk Scale

ABSTRACT The objective of this research was to develop fertility life tables in order to estimate the population parameters of black aphid (Aphis craccivora Koch) in cowpea (Vigna unguiculata) varieties, aiming to propose a risk scale for its use. The experiment consisted of six treatments and six replicates (five varieties plus the cultivar VITA 7 as a susceptible control). A cohort was formed with six adult females distributed in six replicates of each genotype, and the insects were observed daily. Based on the data, fertility life tables were drawn for each variety and the population parameters were estimated. The different values of the finite growth rate (λ) were considered to propose a risk scale for the use of the genotypes. The results obtained give the dimension of the variability of V. unguiculata in respect to the character, resistance to A. craccivora, with antibiosis as the main mechanism of resistance. Considering all the results, the varieties studied can be classified according to their suitability as a plant favorable to the development of the black aphid as follows: VITA 7 > CE-13 > CE-51 > CE-08 = CE-07. The proposal of a risk scale for the use of V. unguiculata genotypes against the A. craccivora population, based on the finite growth rate (λ) values, was adequate to discriminate the varieties studied.

scholarly journals Growth Pattern, Mortality and Exploitation Rate of the Giant African Threadfin, Polydactylus quadrifilis (Cuvier, 1829) from Ebrié Lagoon (Potou Sector, Côte d’Ivoire)

2020 ◽  
pp. 33-42
Author(s):  
Théophile Aké Bédia ◽  
Bakari Coulibaly ◽  
Yao Aristide Konan ◽  
Essetchi Paul Kouamelan ◽  
Valentin N’douba
Keyword(s):  
Growth Rate ◽  
Mortality Rate ◽  
Growth Pattern ◽  
Total Mortality ◽  
Fishing Effort ◽  
Natural Mortality ◽  
Fishing Mortality ◽  
Population Parameters ◽  
Exploitation Rate ◽  
First Maturity

The study evaluated some population parameters of Polydactylus quadrifilis within Ebrié lagoon (Potou sector). Samples were obtained using artisanal gillnet fishery from April 2004 to March 2006. A total of 741 individuals of P. quadrifilis ranged from 11 to 70 cm were examined. Population parameters were estimated where asymptotic length (L∞) was found 60 cm, growth rate (K) 0.33 per year, the longevity (T max) 9.09 years, and growth performance index (Φ′) 3.06. The length at first capture (Lc50 = 10.60 cm) was lower than the length at first maturity (Lm50 = 40 cm). Total mortality rate (Z) was calculated as 1.10 per year including natural mortality and fishing mortality. The exploitation rate (E=0.36) was found to be less than the maximum exploitation rate (E max = 0.44) and indicated that P. quadrifilis is not overexploited. The current exploitation rate should be maintained by sustainable fisheries measures including monitoring of fishing effort.

scholarly journals Aberrant regulation of RNA splicing in sunflower hybrids may underlie intrinsic incompatibilities

2020 ◽  
Author(s):  
Chris C R Smith ◽  
Loren H Rieseberg ◽  
Brent S Hulke ◽  
Nolan C Kane
Keyword(s):  
Growth Rate ◽  
Rna Splicing ◽  
Plant Traits ◽  
Splice Variants ◽  
Single Gene ◽  
Genetic Regulation ◽  
Multiple Alleles ◽  
The Individual ◽  
Multicellular Organisms ◽  
Splice Forms

AbstractAlternative spicing is an integral part of gene expression in multicellular organisms that allows for diverse mRNA transcripts and proteins to be produced from a single gene. However, most existing analyses have focused on macro-evolution, with only limited research on splice site evolution over shorter term, micro-evolutionary time scales. Here we examine splicing evolution that has occurred during domestication and observe 45 novel splice forms with strongly transgressive isoform compositions, representing 0.24% of analyzed transcripts. We identify loci associated with variation in the levels of these splice forms, finding that many novel transcripts were regulated by multiple alleles with non-additive interactions. A subset of these interactions involved the expression of individual spliceosome components. These overdominant and epistatic interactions often resulted in alteration in the protein-coding regions of the transcripts, resulting in frameshifts and truncations. By associating the splice variation in these genes with size and growth rate measurements, we found that none of the individual splice variants affected these plant traits significantly, but the cumulative expression of all aberrant transcripts did show a significant reduction in growth rate associated with higher proportions of disrupted transcripts. This demonstrates the importance of co-evolution of the different spliceosomal components and their regulators and suggests that these genes may contribute to evolution of reproductive isolation as Bateson-Dobzhansky-Muller incompatibility loci.Author summaryIn multicellular organisms, it is common that segments of pre-mRNA molecules are physically removed, and the remaining segments are spliced back together. Through splicing alternative combinations of segments together, organisms produce various mRNA molecules, and thus multiple proteins, using the information encoded in a single gene. Here, we investigated the RNA of two sunflower genotypes, one wild and one domesticated, as well as the hybrid offspring resulting from a cross between the two genotypes. We found certain mRNA molecules that were spliced exclusively in the hybrids and were absent in the examined parental lines. These unique hybrid mRNAs were predicted to be consequential for the hybrids’ health, and thus represented a malfunction in the mechanisms that regulate splicing. These results improve our understanding of the genetic regulation of alternative splicing and how alternative splice forms evolve. Our findings may lead to further inquiries about how aberrant splicing promotes the formation of new species in nature.

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